Vegan-specific signature implies healthier metabolic profile: findings from diet-related multi-omics observational study based on different European populations

Statistical report for microbiome analysis


Authors and affiliations

Monika Cahova1,*, Anna Ouradova2,*, Giulio Ferrero3,4,*, Miriam Bratova1, Nikola Daskova1, Klara Dohnalova5, Marie Heczkova1, Karel Chalupsky5, Maria Kralova6,7, Marek Kuzma8, Filip Tichanek1, Lucie Najmanova8, Barbara Pardini10, Helena Pelantová8, Radislav Sedlacek5, Sonia Tarallo9, Petra Videnska10, Jan Gojda2,#, Alessio Naccarati9,#


* These authors have contributed equally to this work and share first authorship
# These authors have contributed equally to this work and share last authorship

1 Institute for Clinical and Experimental Medicine, Prague, Czech Republic
2 Department of Internal Medicine, Kralovske Vinohrady University Hospital and Third Faculty of Medicine, Charles University, Prague, Czech Republic 3 Department of Clinical and Biological Sciences, University of Turin, Turin, Italy
4 Department of Computer Science, University of Turin, Turin, Italy
5 Czech Centre for Phenogenomics, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czech Republic
6 Ambis University, Department of Economics and Management, Prague, Czech Republic
7 Department of Applied Mathematics and Computer Science, Masaryk University, Brno, Czech Republic
8 Institute of Microbiology of the Czech Academy of Sciences, Prague, Czech Republic
9 Italian Institute for Genomic Medicine (IIGM), c/o IRCCS Candiolo, Turin, Italy
10 Mendel University, Department of Chemistry and Biochemistry, Brno, Czech Republic


This is a statistical report of the study Vegan-specific signature implies healthier metabolic profile: findings from diet-related multi-omics observational study based on different European populations that has been submitted to [TO BE ADDED]

When using this code or data, cite the original publication:

TO BE ADDED

BibTex citation for the original publication:

TO BE ADDED


Original GitHub repository: https://github.com/filip-tichanek/ItCzVegans

Statistical reports can be found on the reports hub.

Data analysis is described in detail in the statistical methods report.


1 Introduction

This project explores potential signatures of a vegan diet across the microbiome, metabolome, and lipidome. We used data from healthy vegan and omnivorous human subjects in two countries (Czech Republic and Italy), with subjects grouped by Country and Diet, resulting in four distinct groups.

To assess the generalizability of these findings, we validated our results with an independent cohort from the Czech Republic for external validation.

1.1 Statistical Methods

The statistical modeling approach is described in detail in this report. Briefly, the methods used included:

  • Multivariate analysis: We conducted multivariate analyses (PERMANOVA, PCA, correlation analyses) to explore the effects of diet, country, and their possible interaction (diet : country) on the microbiome, lipidome, and metabolome compositions in an integrative manner. This part of the analysis is not available on the GitHub page, but the code will be provided upon request.

  • Linear models: Linear models were applied to estimate the effects of diet, country, and their interaction (diet:country) on individual lipids, metabolites, and bacterial taxa (“features”). Features that significantly differed between diet groups (based on the estimated average effect of diet across both countries, adjusted for multiple comparisons with FDR < 0.1) were further examined in the independent validation cohort to assess whether these associations were reproducible.

  • Predictive models (elastic net): We employed elastic net (regularized) logistic regression to predict vegan status based on microbiome, metabolome, and lipidome features (one predictive model per dataset, i.e., three elastic net models in total). These models were internally validated using out-of-bag bootstrap resampling. The discriminatory power of each model to differentiate between diet groups was evaluated using the out-of-sample (optimism-corrected) area under the receiver operating characteristic curve (ROC-AUC). The models trained on the training data were then used to estimate the predicted probability that a given subject is vegan in an indepedent validation cohort. This predicted probability was subsequently used as a variable to discriminate between diet groups for external validation.

2 Initiation

2.1 Set home directory

Open code

setwd('/home/ticf/GitRepo/ticf/478_MOCA_italian')

2.2 Upload initiation file

Open code
source('478_initiation.R')

3 Data

3.1 Upload all original data

3.1.1 Training set

3.1.1.1 Connect metadata from lipidom table

Open code
training_metadata <- read.xlsx('gitignore/data/lipidome_training_cohort.xlsx') %>% 
  select(Sample, Country, Diet) %>% 
  mutate(ID = Sample)

3.1.1.2 Connect italian data

Open code
data_microbiome_IT <- read.table(
  'gitignore/data/0_Data_Metaphlan4_species_filtered_IT_rel_ab.txt') %>%  t()
colnames(data_microbiome_IT) <- data_microbiome_IT[1,]

data_microbiome_IT <- data_microbiome_IT[-1,] %>% data.frame() %>% 
  mutate(
    across(
      Adlercreutzia_equolifaciens:Veillonella_atypica, ~ as.numeric(.)/100
      )
  ) %>% 
  left_join(training_metadata, by = 'ID') %>% 
  select(Sample, Country, Diet, everything()) %>% 
  select(-ID)

3.1.1.3 Connect czech data

Open code
data_microbiome_CZ <- read.table(
  'gitignore/data/0_Data_Metaphlan4_species_filtered_Triema_rel_ab.txt') %>%  t()
colnames(data_microbiome_CZ) <- data_microbiome_CZ[1,]

data_microbiome_CZ <- data_microbiome_CZ[-1,] %>% data.frame() 

data_microbiome_CZ <- data_microbiome_CZ %>% 
  mutate(
    across(
      Adlercreutzia_equolifaciens:Veillonella_atypica, ~ as.numeric(.)/100
      )
  ) %>% 
  left_join(training_metadata, by = 'ID') %>% 
  select(Sample, Country, Diet, everything()) %>% 
  select(-ID)

3.1.1.4 Merging czech and italian data

Open code
data_microbiome_original_raw <- bind_rows(data_microbiome_CZ, data_microbiome_IT)

summary(data_microbiome_original_raw)
##     Sample            Country              Diet          
##  Length:166         Length:166         Length:166        
##  Class :character   Class :character   Class :character  
##  Mode  :character   Mode  :character   Mode  :character  
##                                                          
##                                                          
##                                                          
##  Adlercreutzia_equolifaciens Agathobaculum_butyriciproducens
##  Min.   :0.000e+00           Min.   :0.000000               
##  1st Qu.:0.000e+00           1st Qu.:0.001169               
##  Median :3.445e-05           Median :0.002145               
##  Mean   :2.322e-04           Mean   :0.003461               
##  3rd Qu.:1.853e-04           3rd Qu.:0.004470               
##  Max.   :4.875e-03           Max.   :0.025249               
##  Akkermansia_muciniphila Alistipes_communis Alistipes_finegoldii
##  Min.   :0.0000000       Min.   :0.000000   Min.   :0.000e+00   
##  1st Qu.:0.0000000       1st Qu.:0.000241   1st Qu.:2.220e-06   
##  Median :0.0009167       Median :0.002489   Median :6.484e-04   
##  Mean   :0.0114990       Mean   :0.005551   Mean   :3.641e-03   
##  3rd Qu.:0.0089904       3rd Qu.:0.006985   3rd Qu.:3.530e-03   
##  Max.   :0.2719445       Max.   :0.062301   Max.   :4.998e-02   
##  Alistipes_ihumii    Alistipes_indistinctus Alistipes_onderdonkii
##  Min.   :0.0000000   Min.   :0.0000000      Min.   :0.0000000    
##  1st Qu.:0.0000000   1st Qu.:0.0000000      1st Qu.:0.0003857    
##  Median :0.0004706   Median :0.0000867      Median :0.0031382    
##  Mean   :0.0023185   Mean   :0.0007937      Mean   :0.0145942    
##  3rd Qu.:0.0025642   3rd Qu.:0.0006787      3rd Qu.:0.0122375    
##  Max.   :0.0252111   Max.   :0.0220987      Max.   :0.1750433    
##  Alistipes_putredinis Alistipes_senegalensis Alistipes_shahii  
##  Min.   :0.000000     Min.   :0.000e+00      Min.   :0.000000  
##  1st Qu.:0.001969     1st Qu.:0.000e+00      1st Qu.:0.001151  
##  Median :0.020323     Median :5.500e-07      Median :0.005118  
##  Mean   :0.031732     Mean   :1.014e-03      Mean   :0.009767  
##  3rd Qu.:0.047024     3rd Qu.:8.605e-04      3rd Qu.:0.014467  
##  Max.   :0.162515     Max.   :4.685e-02      Max.   :0.065784  
##  Anaerobutyricum_hallii Anaerofilum_hominis Anaeromassilibacillus_senegalensis
##  Min.   :0.000000       Min.   :0.000e+00   Min.   :0.000e+00                 
##  1st Qu.:0.000000       1st Qu.:0.000e+00   1st Qu.:0.000e+00                 
##  Median :0.000200       Median :0.000e+00   Median :4.750e-06                 
##  Mean   :0.001199       Mean   :3.592e-05   Mean   :9.213e-05                 
##  3rd Qu.:0.001499       3rd Qu.:1.245e-05   3rd Qu.:7.705e-05                 
##  Max.   :0.010241       Max.   :1.020e-03   Max.   :4.582e-03                 
##  Anaerostipes_hadrus Anaerotignum_faecicola Anaerotruncus_colihominis
##  Min.   :0.000e+00   Min.   :0.0000000      Min.   :0.0000000        
##  1st Qu.:3.192e-05   1st Qu.:0.0000000      1st Qu.:0.0000000        
##  Median :8.779e-04   Median :0.0001417      Median :0.0000033        
##  Mean   :4.366e-03   Mean   :0.0016793      Mean   :0.0001279        
##  3rd Qu.:3.934e-03   3rd Qu.:0.0011429      3rd Qu.:0.0001127        
##  Max.   :6.649e-02   Max.   :0.0325208      Max.   :0.0032344        
##  Anaerotruncus_massiliensis Anaerotruncus_rubiinfantis Bacteroides_caccae 
##  Min.   :0.000e+00          Min.   :0.000e+00          Min.   :0.0000000  
##  1st Qu.:0.000e+00          1st Qu.:0.000e+00          1st Qu.:0.0000000  
##  Median :0.000e+00          Median :1.350e-05          Median :0.0008121  
##  Mean   :5.832e-05          Mean   :5.911e-05          Mean   :0.0036313  
##  3rd Qu.:7.850e-06          3rd Qu.:8.100e-05          3rd Qu.:0.0035346  
##  Max.   :1.608e-03          Max.   :4.332e-04          Max.   :0.0596008  
##  Bacteroides_cellulosilyticus Bacteroides_clarus  Bacteroides_eggerthii
##  Min.   :0.0000000            Min.   :0.0000000   Min.   :0.0000000    
##  1st Qu.:0.0000000            1st Qu.:0.0000000   1st Qu.:0.0000000    
##  Median :0.0000053            Median :0.0000000   Median :0.0000000    
##  Mean   :0.0033031            Mean   :0.0017244   Mean   :0.0028440    
##  3rd Qu.:0.0009843            3rd Qu.:0.0002202   3rd Qu.:0.0007432    
##  Max.   :0.0949794            Max.   :0.1004693   Max.   :0.0553489    
##  Bacteroides_fragilis Bacteroides_ovatus  Bacteroides_stercoris
##  Min.   :0.0000000    Min.   :0.0000000   Min.   :0.0000000    
##  1st Qu.:0.0000000    1st Qu.:0.0003829   1st Qu.:0.0000000    
##  Median :0.0000000    Median :0.0018786   Median :0.0000088    
##  Mean   :0.0013740    Mean   :0.0087568   Mean   :0.0110969    
##  3rd Qu.:0.0002518    3rd Qu.:0.0080833   3rd Qu.:0.0044142    
##  Max.   :0.0527658    Max.   :0.1835700   Max.   :0.1933994    
##  Bacteroides_thetaiotaomicron Bacteroides_uniformis Bacteroides_xylanisolvens
##  Min.   :0.000e+00            Min.   :0.00000       Min.   :0.000e+00        
##  1st Qu.:2.998e-05            1st Qu.:0.00478       1st Qu.:1.432e-05        
##  Median :5.684e-04            Median :0.01814       Median :1.836e-04        
##  Mean   :2.592e-03            Mean   :0.03531       Mean   :2.843e-03        
##  3rd Qu.:2.370e-03            3rd Qu.:0.04496       3rd Qu.:1.746e-03        
##  Max.   :4.940e-02            Max.   :0.20757       Max.   :1.622e-01        
##  Barnesiella_intestinihominis Bifidobacterium_adolescentis
##  Min.   :0.000e+00            Min.   :0.000e+00           
##  1st Qu.:5.347e-05            1st Qu.:3.222e-05           
##  Median :1.172e-03            Median :2.265e-03           
##  Mean   :3.144e-03            Mean   :6.628e-03           
##  3rd Qu.:3.539e-03            3rd Qu.:8.386e-03           
##  Max.   :2.845e-02            Max.   :7.717e-02           
##  Bifidobacterium_longum Bilophila_SGB15451  Bilophila_wadsworthia
##  Min.   :0.0000000      Min.   :0.0000000   Min.   :0.0000000    
##  1st Qu.:0.0003053      1st Qu.:0.0000000   1st Qu.:0.0001018    
##  Median :0.0016524      Median :0.0000000   Median :0.0005542    
##  Mean   :0.0059831      Mean   :0.0001598   Mean   :0.0015594    
##  3rd Qu.:0.0040142      3rd Qu.:0.0000000   3rd Qu.:0.0018417    
##  Max.   :0.1582122      Max.   :0.0048426   Max.   :0.0194645    
##  Blautia_faecis      Blautia_glucerasea  Blautia_massiliensis
##  Min.   :0.0000000   Min.   :0.000e+00   Min.   :0.0000000   
##  1st Qu.:0.0000874   1st Qu.:9.875e-06   1st Qu.:0.0000000   
##  Median :0.0004041   Median :1.647e-04   Median :0.0001212   
##  Mean   :0.0013417   Mean   :4.602e-04   Mean   :0.0018358   
##  3rd Qu.:0.0013706   3rd Qu.:5.990e-04   3rd Qu.:0.0013415   
##  Max.   :0.0327014   Max.   :5.534e-03   Max.   :0.0664897   
##  Blautia_obeum       Blautia_sp_MCC283   Blautia_wexlerae  
##  Min.   :0.0000000   Min.   :0.000e+00   Min.   :0.000000  
##  1st Qu.:0.0000492   1st Qu.:0.000e+00   1st Qu.:0.000149  
##  Median :0.0002816   Median :9.185e-05   Median :0.001101  
##  Mean   :0.0010843   Mean   :1.117e-03   Mean   :0.005289  
##  3rd Qu.:0.0011403   3rd Qu.:6.552e-04   3rd Qu.:0.004533  
##  Max.   :0.0230052   Max.   :7.301e-02   Max.   :0.117828  
##  Brotolimicola_acetigignens Butyricimonas_faecihominis Butyricimonas_virosa
##  Min.   :0.0000000          Min.   :0.0000000          Min.   :0.0000000   
##  1st Qu.:0.0002889          1st Qu.:0.0000000          1st Qu.:0.0000000   
##  Median :0.0010865          Median :0.0000000          Median :0.0000000   
##  Mean   :0.0065503          Mean   :0.0002135          Mean   :0.0001199   
##  3rd Qu.:0.0043654          3rd Qu.:0.0001897          3rd Qu.:0.0000636   
##  Max.   :0.1078520          Max.   :0.0046050          Max.   :0.0038677   
##  Candidatus_Borkfalkia_ceftriaxoniphila Candidatus_Cibionibacter_quicibialis
##  Min.   :0.000e+00                      Min.   :0.000000                    
##  1st Qu.:0.000e+00                      1st Qu.:0.002497                    
##  Median :0.000e+00                      Median :0.008757                    
##  Mean   :2.061e-04                      Mean   :0.016591                    
##  3rd Qu.:2.572e-05                      3rd Qu.:0.018056                    
##  Max.   :5.555e-03                      Max.   :0.160329                    
##  Clostridia_bacterium_UC5_1_1D1 Clostridiaceae_bacterium
##  Min.   :0.000e+00              Min.   :0.0000000       
##  1st Qu.:0.000e+00              1st Qu.:0.0001688       
##  Median :9.200e-06              Median :0.0009697       
##  Mean   :6.736e-05              Mean   :0.0027794       
##  3rd Qu.:5.440e-05              3rd Qu.:0.0033770       
##  Max.   :1.829e-03              Max.   :0.0288186       
##  Clostridiaceae_bacterium_AF18_31LB Clostridiaceae_bacterium_Marseille_Q4143
##  Min.   :0.0000000                  Min.   :0.000e+00                       
##  1st Qu.:0.0000653                  1st Qu.:5.650e-06                       
##  Median :0.0002154                  Median :6.825e-05                       
##  Mean   :0.0005095                  Mean   :1.843e-04                       
##  3rd Qu.:0.0005462                  3rd Qu.:2.342e-04                       
##  Max.   :0.0083933                  Max.   :1.895e-03                       
##  Clostridiaceae_bacterium_Marseille_Q4145 Clostridiales_bacterium
##  Min.   :0.000e+00                        Min.   :0.0000000      
##  1st Qu.:0.000e+00                        1st Qu.:0.0000266      
##  Median :1.720e-05                        Median :0.0002925      
##  Mean   :6.544e-05                        Mean   :0.0010598      
##  3rd Qu.:7.700e-05                        3rd Qu.:0.0011261      
##  Max.   :8.947e-04                        Max.   :0.0299120      
##  Clostridiales_bacterium_KLE1615 Clostridium_SGB4750 Clostridium_SGB4909
##  Min.   :0.000e+00               Min.   :0.000e+00   Min.   :0.0000000  
##  1st Qu.:5.265e-05               1st Qu.:7.420e-06   1st Qu.:0.0000000  
##  Median :5.064e-04               Median :8.570e-05   Median :0.0000000  
##  Mean   :1.227e-03               Mean   :1.011e-03   Mean   :0.0008375  
##  3rd Qu.:1.685e-03               3rd Qu.:6.413e-04   3rd Qu.:0.0001642  
##  Max.   :1.037e-02               Max.   :4.993e-02   Max.   :0.0359632  
##  Clostridium_fessum  Clostridium_leptum  Clostridium_sp_AF20_17LB
##  Min.   :0.0000000   Min.   :0.000e+00   Min.   :0.000e+00       
##  1st Qu.:0.0005066   1st Qu.:0.000e+00   1st Qu.:2.498e-05       
##  Median :0.0015853   Median :3.415e-05   Median :2.959e-04       
##  Mean   :0.0035494   Mean   :4.016e-04   Mean   :8.341e-04       
##  3rd Qu.:0.0040255   3rd Qu.:1.088e-04   3rd Qu.:1.096e-03       
##  Max.   :0.0510927   Max.   :3.291e-02   Max.   :7.102e-03       
##  Clostridium_sp_AF27_2AA Clostridium_sp_AF36_4 Clostridium_sp_AM22_11AC
##  Min.   :0.0000000       Min.   :0.0000000     Min.   :0.0000000       
##  1st Qu.:0.0000000       1st Qu.:0.0000000     1st Qu.:0.0001011       
##  Median :0.0001306       Median :0.0001521     Median :0.0005213       
##  Mean   :0.0007414       Mean   :0.0022566     Mean   :0.0021444       
##  3rd Qu.:0.0004987       3rd Qu.:0.0014196     3rd Qu.:0.0021354       
##  Max.   :0.0175781       Max.   :0.0835989     Max.   :0.0263489       
##  Clostridium_sp_AM33_3 Collinsella_aerofaciens Coprobacter_fastidiosus
##  Min.   :0.000e+00     Min.   :0.0000000       Min.   :0.0000000      
##  1st Qu.:6.235e-05     1st Qu.:0.0002452       1st Qu.:0.0000000      
##  Median :3.146e-04     Median :0.0008033       Median :0.0000000      
##  Mean   :8.151e-04     Mean   :0.0017892       Mean   :0.0002232      
##  3rd Qu.:7.753e-04     3rd Qu.:0.0022898       3rd Qu.:0.0001505      
##  Max.   :1.569e-02     Max.   :0.0235808       Max.   :0.0065932      
##  Coprococcus_catus   Coprococcus_comes   Coprococcus_eutactus
##  Min.   :0.000e+00   Min.   :0.000e+00   Min.   :0.0000000   
##  1st Qu.:2.735e-05   1st Qu.:1.875e-05   1st Qu.:0.0000000   
##  Median :3.185e-04   Median :2.600e-04   Median :0.0007131   
##  Mean   :5.147e-04   Mean   :9.327e-04   Mean   :0.0052089   
##  3rd Qu.:6.389e-04   3rd Qu.:8.071e-04   3rd Qu.:0.0052116   
##  Max.   :5.175e-03   Max.   :1.307e-02   Max.   :0.1018948   
##  Dorea_formicigenerans Dorea_longicatena   Dorea_sp_AF36_15AT 
##  Min.   :0.000e+00     Min.   :0.000e+00   Min.   :0.0000000  
##  1st Qu.:6.925e-06     1st Qu.:4.225e-05   1st Qu.:0.0000000  
##  Median :1.640e-04     Median :5.707e-04   Median :0.0000212  
##  Mean   :4.927e-04     Mean   :1.745e-03   Mean   :0.0001276  
##  3rd Qu.:6.154e-04     3rd Qu.:2.034e-03   3rd Qu.:0.0001202  
##  Max.   :5.509e-03     Max.   :3.282e-02   Max.   :0.0018086  
##  Dysosmobacter_SGB15077 Dysosmobacter_welbionis Eggerthella_lenta  
##  Min.   :0.000e+00      Min.   :0.0000000       Min.   :0.000e+00  
##  1st Qu.:0.000e+00      1st Qu.:0.0002946       1st Qu.:0.000e+00  
##  Median :0.000e+00      Median :0.0010386       Median :0.000e+00  
##  Mean   :3.268e-04      Mean   :0.0029821       Mean   :1.296e-04  
##  3rd Qu.:1.722e-05      3rd Qu.:0.0040171       3rd Qu.:3.222e-05  
##  Max.   :1.258e-02      Max.   :0.0421230       Max.   :5.440e-03  
##  Enterocloster_citroniae Enterocloster_hominis Escherichia_coli   
##  Min.   :0.0000000       Min.   :0.0000000     Min.   :0.0000000  
##  1st Qu.:0.0000000       1st Qu.:0.0000000     1st Qu.:0.0000000  
##  Median :0.0000150       Median :0.0000000     Median :0.0001308  
##  Mean   :0.0001126       Mean   :0.0005085     Mean   :0.0013753  
##  3rd Qu.:0.0000869       3rd Qu.:0.0001440     3rd Qu.:0.0006760  
##  Max.   :0.0021971       Max.   :0.0111120     Max.   :0.0522880  
##  Eubacterium_ramulus Eubacterium_rectale Eubacterium_siraeum
##  Min.   :0.0000000   Min.   :0.000000    Min.   :0.0000000  
##  1st Qu.:0.0000000   1st Qu.:0.001165    1st Qu.:0.0000000  
##  Median :0.0000805   Median :0.005220    Median :0.0000000  
##  Mean   :0.0002872   Mean   :0.014922    Mean   :0.0012085  
##  3rd Qu.:0.0002941   3rd Qu.:0.016470    3rd Qu.:0.0002872  
##  Max.   :0.0034632   Max.   :0.109626    Max.   :0.0352094  
##  Eubacterium_ventriosum Faecalibacterium_SGB15346 Faecalibacterium_prausnitzii
##  Min.   :0.000e+00      Min.   :0.0000000         Min.   :0.00000             
##  1st Qu.:0.000e+00      1st Qu.:0.0005724         1st Qu.:0.02017             
##  Median :6.945e-05      Median :0.0029065         Median :0.04250             
##  Mean   :8.707e-04      Mean   :0.0063215         Mean   :0.05886             
##  3rd Qu.:5.903e-04      3rd Qu.:0.0085679         3rd Qu.:0.08075             
##  Max.   :2.029e-02      Max.   :0.0799532         Max.   :0.33216             
##  Faecalibacterium_sp_CLA_AA_H233 Faecalibacterium_sp_HTFF
##  Min.   :0.000e+00               Min.   :0.000e+00       
##  1st Qu.:4.850e-06               1st Qu.:0.000e+00       
##  Median :2.348e-04               Median :7.785e-05       
##  Mean   :2.630e-03               Mean   :1.182e-03       
##  3rd Qu.:1.499e-03               3rd Qu.:1.062e-03       
##  Max.   :5.355e-02               Max.   :2.208e-02       
##  Faecalicatena_fissicatena Flavonifractor_plautii
##  Min.   :0.000e+00         Min.   :0.000e+00     
##  1st Qu.:1.585e-05         1st Qu.:3.105e-05     
##  Median :3.200e-04         Median :2.823e-04     
##  Mean   :1.050e-03         Mean   :1.355e-03     
##  3rd Qu.:1.174e-03         3rd Qu.:1.116e-03     
##  Max.   :1.405e-02         Max.   :2.862e-02     
##  Fusicatenibacter_saccharivorans Fusicatenibacter_sp_CLA_AA_H277
##  Min.   :0.000000                Min.   :0.000e+00              
##  1st Qu.:0.001050                1st Qu.:5.675e-05              
##  Median :0.002624                Median :2.263e-04              
##  Mean   :0.004965                Mean   :4.027e-04              
##  3rd Qu.:0.005350                3rd Qu.:5.232e-04              
##  Max.   :0.061662                Max.   :4.875e-03              
##  GGB13404_SGB14252   GGB1420_SGB1957     GGB2653_SGB3574    
##  Min.   :0.000e+00   Min.   :0.0000000   Min.   :0.0000000  
##  1st Qu.:0.000e+00   1st Qu.:0.0000000   1st Qu.:0.0000000  
##  Median :3.350e-06   Median :0.0000000   Median :0.0000241  
##  Mean   :1.583e-04   Mean   :0.0003116   Mean   :0.0001354  
##  3rd Qu.:1.745e-04   3rd Qu.:0.0000000   3rd Qu.:0.0001323  
##  Max.   :2.198e-03   Max.   :0.0079631   Max.   :0.0044801  
##  GGB2998_SGB3988     GGB3034_SGB4030     GGB3109_SGB4121    
##  Min.   :0.0000000   Min.   :0.000e+00   Min.   :0.000e+00  
##  1st Qu.:0.0000000   1st Qu.:0.000e+00   1st Qu.:0.000e+00  
##  Median :0.0000000   Median :0.000e+00   Median :8.050e-06  
##  Mean   :0.0001071   Mean   :1.096e-05   Mean   :4.249e-04  
##  3rd Qu.:0.0000801   3rd Qu.:0.000e+00   3rd Qu.:3.460e-04  
##  Max.   :0.0025680   Max.   :2.346e-04   Max.   :6.376e-03  
##  GGB3175_SGB4191     GGB33469_SGB15236   GGB33512_SGB15203  
##  Min.   :0.0000000   Min.   :0.000e+00   Min.   :0.000e+00  
##  1st Qu.:0.0000000   1st Qu.:0.000e+00   1st Qu.:0.000e+00  
##  Median :0.0000000   Median :3.005e-05   Median :0.000e+00  
##  Mean   :0.0028154   Mean   :1.712e-03   Mean   :7.039e-04  
##  3rd Qu.:0.0004661   3rd Qu.:1.273e-03   3rd Qu.:5.617e-05  
##  Max.   :0.0515210   Max.   :4.202e-02   Max.   :4.454e-02  
##  GGB33586_SGB53517   GGB3537_SGB4727     GGB38744_SGB14842  
##  Min.   :0.0000000   Min.   :0.000e+00   Min.   :0.000e+00  
##  1st Qu.:0.0000000   1st Qu.:0.000e+00   1st Qu.:0.000e+00  
##  Median :0.0000000   Median :0.000e+00   Median :0.000e+00  
##  Mean   :0.0002087   Mean   :3.764e-05   Mean   :5.670e-06  
##  3rd Qu.:0.0001938   3rd Qu.:1.915e-05   3rd Qu.:0.000e+00  
##  Max.   :0.0039798   Max.   :1.368e-03   Max.   :1.931e-04  
##  GGB45432_SGB63101   GGB45613_SGB63326   GGB47687_SGB2286   
##  Min.   :0.000e+00   Min.   :0.000e+00   Min.   :0.0000000  
##  1st Qu.:0.000e+00   1st Qu.:0.000e+00   1st Qu.:0.0000000  
##  Median :3.050e-06   Median :0.000e+00   Median :0.0000000  
##  Mean   :3.901e-05   Mean   :1.626e-05   Mean   :0.0028797  
##  3rd Qu.:4.275e-05   3rd Qu.:1.217e-05   3rd Qu.:0.0007292  
##  Max.   :8.899e-04   Max.   :7.168e-04   Max.   :0.1126518  
##  GGB52106_SGB72838   GGB52130_SGB14966   GGB9062_SGB13981   
##  Min.   :0.000e+00   Min.   :0.000e+00   Min.   :0.0000000  
##  1st Qu.:0.000e+00   1st Qu.:0.000e+00   1st Qu.:0.0000000  
##  Median :0.000e+00   Median :7.395e-05   Median :0.0000000  
##  Mean   :3.494e-05   Mean   :1.876e-04   Mean   :0.0001584  
##  3rd Qu.:1.155e-05   3rd Qu.:2.760e-04   3rd Qu.:0.0000683  
##  Max.   :9.622e-04   Max.   :2.031e-03   Max.   :0.0022193  
##  GGB9063_SGB13982    GGB9064_SGB13983    GGB9342_SGB14306    GGB9345_SGB14311  
##  Min.   :0.0000000   Min.   :0.0000000   Min.   :0.000e+00   Min.   :0.000000  
##  1st Qu.:0.0000000   1st Qu.:0.0000000   1st Qu.:0.000e+00   1st Qu.:0.000000  
##  Median :0.0000000   Median :0.0000000   Median :7.350e-06   Median :0.000000  
##  Mean   :0.0003579   Mean   :0.0004445   Mean   :1.645e-03   Mean   :0.001554  
##  3rd Qu.:0.0001142   3rd Qu.:0.0001410   3rd Qu.:7.287e-04   3rd Qu.:0.000609  
##  Max.   :0.0179030   Max.   :0.0136173   Max.   :3.655e-02   Max.   :0.030108  
##  GGB9453_SGB14844    GGB9502_SGB14899    GGB9509_SGB14906   
##  Min.   :0.0000000   Min.   :0.0000000   Min.   :0.0000000  
##  1st Qu.:0.0000000   1st Qu.:0.0000000   1st Qu.:0.0000000  
##  Median :0.0000000   Median :0.0000000   Median :0.0000000  
##  Mean   :0.0001438   Mean   :0.0002479   Mean   :0.0005623  
##  3rd Qu.:0.0000136   3rd Qu.:0.0003216   3rd Qu.:0.0002062  
##  Max.   :0.0160739   Max.   :0.0053168   Max.   :0.0298472  
##  GGB9522_SGB14921    GGB9531_SGB14932    GGB9534_SGB14937    GGB9602_SGB15031  
##  Min.   :0.000e+00   Min.   :0.000e+00   Min.   :0.0000000   Min.   :0.000000  
##  1st Qu.:0.000e+00   1st Qu.:0.000e+00   1st Qu.:0.0000000   1st Qu.:0.000000  
##  Median :0.000e+00   Median :0.000e+00   Median :0.0000369   Median :0.000073  
##  Mean   :8.645e-05   Mean   :8.689e-05   Mean   :0.0003241   Mean   :0.002779  
##  3rd Qu.:6.947e-05   3rd Qu.:5.728e-05   3rd Qu.:0.0002522   3rd Qu.:0.001375  
##  Max.   :2.344e-03   Max.   :1.621e-03   Max.   :0.0118852   Max.   :0.057453  
##  GGB9614_SGB15049    GGB9619_SGB15067    GGB9621_SGB15073   
##  Min.   :0.000e+00   Min.   :0.0000000   Min.   :0.0000000  
##  1st Qu.:2.925e-06   1st Qu.:0.0000000   1st Qu.:0.0000000  
##  Median :3.113e-04   Median :0.0000000   Median :0.0000000  
##  Mean   :1.012e-03   Mean   :0.0001688   Mean   :0.0003440  
##  3rd Qu.:1.303e-03   3rd Qu.:0.0001388   3rd Qu.:0.0004201  
##  Max.   :9.384e-03   Max.   :0.0028069   Max.   :0.0026832  
##  GGB9635_SGB15106    GGB9646_SGB15123    GGB9667_SGB15164   
##  Min.   :0.000e+00   Min.   :0.0000000   Min.   :0.0000000  
##  1st Qu.:0.000e+00   1st Qu.:0.0000000   1st Qu.:0.0000000  
##  Median :2.305e-05   Median :0.0000103   Median :0.0000159  
##  Mean   :1.074e-02   Mean   :0.0001020   Mean   :0.0004053  
##  3rd Qu.:5.986e-03   3rd Qu.:0.0001008   3rd Qu.:0.0003939  
##  Max.   :1.383e-01   Max.   :0.0018468   Max.   :0.0042443  
##  GGB9699_SGB15216    GGB9708_SGB15234    GGB9715_SGB15265   
##  Min.   :0.000e+00   Min.   :0.0000000   Min.   :0.0000000  
##  1st Qu.:4.528e-05   1st Qu.:0.0000000   1st Qu.:0.0000000  
##  Median :3.890e-04   Median :0.0001936   Median :0.0002471  
##  Mean   :1.259e-03   Mean   :0.0037159   Mean   :0.0070566  
##  3rd Qu.:1.726e-03   3rd Qu.:0.0022052   3rd Qu.:0.0063499  
##  Max.   :1.577e-02   Max.   :0.0882956   Max.   :0.1487586  
##  GGB9719_SGB15272    GGB9719_SGB15273    GGB9730_SGB15291    GGB9758_SGB15368  
##  Min.   :0.0000000   Min.   :0.0000000   Min.   :0.0000000   Min.   :0.000000  
##  1st Qu.:0.0000000   1st Qu.:0.0000000   1st Qu.:0.0000550   1st Qu.:0.000000  
##  Median :0.0000000   Median :0.0000000   Median :0.0005648   Median :0.001519  
##  Mean   :0.0001319   Mean   :0.0000583   Mean   :0.0011109   Mean   :0.019032  
##  3rd Qu.:0.0001295   3rd Qu.:0.0000015   3rd Qu.:0.0012614   3rd Qu.:0.022600  
##  Max.   :0.0029524   Max.   :0.0019590   Max.   :0.0122176   Max.   :0.290886  
##  GGB9760_SGB15373    GGB9765_SGB15382    GGB9770_SGB15390   
##  Min.   :0.000e+00   Min.   :0.000e+00   Min.   :0.000e+00  
##  1st Qu.:3.035e-05   1st Qu.:0.000e+00   1st Qu.:0.000e+00  
##  Median :3.542e-04   Median :0.000e+00   Median :0.000e+00  
##  Mean   :8.777e-04   Mean   :6.240e-05   Mean   :1.359e-04  
##  3rd Qu.:9.922e-04   3rd Qu.:1.657e-05   3rd Qu.:5.283e-05  
##  Max.   :1.301e-02   Max.   :1.829e-03   Max.   :4.034e-03  
##  GGB9775_SGB15395    GGB9781_SGB15402    GGB9818_SGB15459   
##  Min.   :0.0000000   Min.   :0.000e+00   Min.   :0.0000000  
##  1st Qu.:0.0000000   1st Qu.:0.000e+00   1st Qu.:0.0000000  
##  Median :0.0000000   Median :0.000e+00   Median :0.0000000  
##  Mean   :0.0002453   Mean   :1.531e-05   Mean   :0.0003090  
##  3rd Qu.:0.0000375   3rd Qu.:2.450e-06   3rd Qu.:0.0001238  
##  Max.   :0.0061360   Max.   :4.557e-04   Max.   :0.0072002  
##  Gemmiger_formicilis Guopingia_tenuis    Holdemania_filiformis
##  Min.   :0.000000    Min.   :0.000e+00   Min.   :0.000e+00    
##  1st Qu.:0.001873    1st Qu.:0.000e+00   1st Qu.:0.000e+00    
##  Median :0.005235    Median :0.000e+00   Median :2.950e-06    
##  Mean   :0.010605    Mean   :2.629e-05   Mean   :1.214e-04    
##  3rd Qu.:0.013073    3rd Qu.:3.280e-05   3rd Qu.:8.608e-05    
##  Max.   :0.124274    Max.   :4.077e-04   Max.   :1.739e-03    
##  Hydrogenoanaerobacterium_saccharovorans Intestinimonas_butyriciproducens
##  Min.   :0.0000000                       Min.   :0.0000000               
##  1st Qu.:0.0000000                       1st Qu.:0.0000000               
##  Median :0.0004149                       Median :0.0000497               
##  Mean   :0.0008410                       Mean   :0.0003672               
##  3rd Qu.:0.0012499                       3rd Qu.:0.0002387               
##  Max.   :0.0068933                       Max.   :0.0076464               
##  Intestinimonas_gabonensis Intestinimonas_massiliensis
##  Min.   :0.000e+00         Min.   :0.000e+00          
##  1st Qu.:0.000e+00         1st Qu.:0.000e+00          
##  Median :3.350e-05         Median :0.000e+00          
##  Mean   :7.254e-05         Mean   :2.710e-04          
##  3rd Qu.:1.120e-04         3rd Qu.:9.995e-05          
##  Max.   :5.578e-04         Max.   :5.890e-03          
##  Lachnoclostridium_sp_An138 Lachnospira_eligens Lachnospira_pectinoschiza
##  Min.   :0.000e+00          Min.   :0.0000000   Min.   :0.0000000        
##  1st Qu.:0.000e+00          1st Qu.:0.0000837   1st Qu.:0.0004423        
##  Median :0.000e+00          Median :0.0010730   Median :0.0024533        
##  Mean   :1.229e-05          Mean   :0.0060395   Mean   :0.0105211        
##  3rd Qu.:0.000e+00          3rd Qu.:0.0060136   3rd Qu.:0.0108216        
##  Max.   :4.719e-04          Max.   :0.0711575   Max.   :0.1491405        
##  Lachnospiraceae_bacterium Lachnospiraceae_bacterium_AM48_27BH
##  Min.   :0.000e+00         Min.   :0.0000000                  
##  1st Qu.:5.312e-05         1st Qu.:0.0000058                  
##  Median :3.161e-04         Median :0.0001449                  
##  Mean   :1.499e-03         Mean   :0.0004808                  
##  3rd Qu.:1.252e-03         3rd Qu.:0.0007510                  
##  Max.   :2.828e-02         Max.   :0.0036770                  
##  Lachnospiraceae_bacterium_CLA_AA_H215 Lachnospiraceae_bacterium_CLA_AA_H244
##  Min.   :0.0000000                     Min.   :0.0000000                    
##  1st Qu.:0.0000000                     1st Qu.:0.0003953                    
##  Median :0.0000196                     Median :0.0011186                    
##  Mean   :0.0001348                     Mean   :0.0030128                    
##  3rd Qu.:0.0001249                     3rd Qu.:0.0027737                    
##  Max.   :0.0017039                     Max.   :0.0417129                    
##  Lachnotalea_sp_AF33_28 Lacrimispora_amygdalina Lawsonibacter_SGB15145
##  Min.   :0.000e+00      Min.   :0.0000000       Min.   :0.0000000     
##  1st Qu.:0.000e+00      1st Qu.:0.0001620       1st Qu.:0.0000000     
##  Median :0.000e+00      Median :0.0006867       Median :0.0000432     
##  Mean   :2.355e-05      Mean   :0.0015083       Mean   :0.0003115     
##  3rd Qu.:1.962e-05      3rd Qu.:0.0018513       3rd Qu.:0.0003499     
##  Max.   :5.779e-04      Max.   :0.0157674       Max.   :0.0043012     
##  Lawsonibacter_asaccharolyticus Lawsonibacter_hominis Ligaoa_zhengdingensis
##  Min.   :0.0000000              Min.   :0.0000000     Min.   :0.000e+00    
##  1st Qu.:0.0000846              1st Qu.:0.0000000     1st Qu.:0.000e+00    
##  Median :0.0004759              Median :0.0000097     Median :0.000e+00    
##  Mean   :0.0019247              Mean   :0.0002159     Mean   :2.402e-05    
##  3rd Qu.:0.0021256              3rd Qu.:0.0001272     3rd Qu.:1.962e-05    
##  Max.   :0.0304000              Max.   :0.0053049     Max.   :2.281e-04    
##  Mediterraneibacter_faecis Odoribacter_splanchnicus Oliverpabstia_intestinalis
##  Min.   :0.000e+00         Min.   :0.0000000        Min.   :0.0000000         
##  1st Qu.:0.000e+00         1st Qu.:0.0001976        1st Qu.:0.0000000         
##  Median :5.955e-05         Median :0.0007932        Median :0.0000556         
##  Mean   :7.432e-04         Mean   :0.0015979        Mean   :0.0006646         
##  3rd Qu.:5.370e-04         3rd Qu.:0.0022577        3rd Qu.:0.0005179         
##  Max.   :1.094e-02         Max.   :0.0104102        Max.   :0.0164907         
##  Oscillibacter_sp_ER4 Oscillibacter_sp_MSJ_31 Oscillibacter_sp_PC13
##  Min.   :0.000e+00    Min.   :0.0000000       Min.   :0.000e+00    
##  1st Qu.:4.378e-05    1st Qu.:0.0000000       1st Qu.:0.000e+00    
##  Median :4.039e-03    Median :0.0009371       Median :0.000e+00    
##  Mean   :9.269e-03    Mean   :0.0061000       Mean   :2.549e-05    
##  3rd Qu.:1.198e-02    3rd Qu.:0.0059364       3rd Qu.:3.142e-05    
##  Max.   :6.875e-02    Max.   :0.1408486       Max.   :2.627e-04    
##  Oscillibacter_valericigenes Oscillospiraceae_bacterium
##  Min.   :0.0000000           Min.   :0.000000          
##  1st Qu.:0.0005627           1st Qu.:0.000000          
##  Median :0.0016343           Median :0.000192          
##  Mean   :0.0037479           Mean   :0.002295          
##  3rd Qu.:0.0045934           3rd Qu.:0.001233          
##  Max.   :0.0462371           Max.   :0.094657          
##  Oscillospiraceae_bacterium_CLA_AA_H250
##  Min.   :0.000e+00                     
##  1st Qu.:3.502e-05                     
##  Median :4.721e-04                     
##  Mean   :1.267e-03                     
##  3rd Qu.:1.347e-03                     
##  Max.   :2.662e-02                     
##  Oscillospiraceae_bacterium_Marseille_Q3528 Parabacteroides_distasonis
##  Min.   :0.0000000                          Min.   :0.0000000         
##  1st Qu.:0.0000000                          1st Qu.:0.0005998         
##  Median :0.0001102                          Median :0.0021084         
##  Mean   :0.0002187                          Mean   :0.0040434         
##  3rd Qu.:0.0002662                          3rd Qu.:0.0055781         
##  Max.   :0.0029340                          Max.   :0.0319649         
##  Parabacteroides_merdae Paraprevotella_clara Parasutterella_excrementihominis
##  Min.   :0.000000       Min.   :0.000e+00    Min.   :0.0000000               
##  1st Qu.:0.000000       1st Qu.:0.000e+00    1st Qu.:0.0000000               
##  Median :0.001745       Median :1.005e-05    Median :0.0000925               
##  Mean   :0.004220       Mean   :3.847e-03    Mean   :0.0016349               
##  3rd Qu.:0.005745       3rd Qu.:5.190e-03    3rd Qu.:0.0007551               
##  Max.   :0.042251       Max.   :6.890e-02    Max.   :0.0317369               
##  Phascolarctobacterium_faecium Phocaeicola_dorei   Phocaeicola_sartorii
##  Min.   :0.000000              Min.   :0.0000000   Min.   :0.000e+00   
##  1st Qu.:0.000000              1st Qu.:0.0000012   1st Qu.:0.000e+00   
##  Median :0.000000              Median :0.0007404   Median :0.000e+00   
##  Mean   :0.005069              Mean   :0.0108577   Mean   :5.930e-06   
##  3rd Qu.:0.001155              3rd Qu.:0.0092181   3rd Qu.:1.575e-06   
##  Max.   :0.143305              Max.   :0.1978448   Max.   :8.170e-05   
##  Phocaeicola_vulgatus Phocea_massiliensis Provencibacterium_massiliense
##  Min.   :0.000000     Min.   :0.000e+00   Min.   :0.000e+00            
##  1st Qu.:0.002865     1st Qu.:0.000e+00   1st Qu.:0.000e+00            
##  Median :0.011614     Median :0.000e+00   Median :0.000e+00            
##  Mean   :0.035908     Mean   :7.498e-05   Mean   :1.407e-05            
##  3rd Qu.:0.038286     3rd Qu.:8.520e-05   3rd Qu.:8.925e-06            
##  Max.   :0.307894     Max.   :1.255e-03   Max.   :2.829e-04            
##  Pseudoflavonifractor_capillosus Roseburia_faecis    Roseburia_hominis  
##  Min.   :0.000e+00               Min.   :0.000e+00   Min.   :0.0000000  
##  1st Qu.:0.000e+00               1st Qu.:6.042e-05   1st Qu.:0.0002858  
##  Median :1.700e-06               Median :1.138e-03   Median :0.0013928  
##  Mean   :2.400e-04               Mean   :7.160e-03   Mean   :0.0040151  
##  3rd Qu.:9.677e-05               3rd Qu.:5.784e-03   3rd Qu.:0.0042910  
##  Max.   :1.109e-02               Max.   :2.296e-01   Max.   :0.0796848  
##  Roseburia_intestinalis Roseburia_inulinivorans Ruminococcus_bicirculans
##  Min.   :0.0000000      Min.   :0.0000000       Min.   :0.0000000       
##  1st Qu.:0.0000000      1st Qu.:0.0002055       1st Qu.:0.0000348       
##  Median :0.0000717      Median :0.0009830       Median :0.0007192       
##  Mean   :0.0021826      Mean   :0.0039152       Mean   :0.0029495       
##  3rd Qu.:0.0011131      3rd Qu.:0.0034006       3rd Qu.:0.0033711       
##  Max.   :0.0499108      Max.   :0.0620626       Max.   :0.0270153       
##  Ruminococcus_bromii Ruminococcus_torques Ruthenibacterium_lactatiformans
##  Min.   :0.0000000   Min.   :0.0000000    Min.   :0.0000000              
##  1st Qu.:0.0000000   1st Qu.:0.0000000    1st Qu.:0.0001935              
##  Median :0.0008906   Median :0.0000008    Median :0.0005254              
##  Mean   :0.0070197   Mean   :0.0005111    Mean   :0.0014620              
##  3rd Qu.:0.0050637   3rd Qu.:0.0002775    3rd Qu.:0.0015064              
##  Max.   :0.1629682   Max.   :0.0149266    Max.   :0.0358279              
##  Segatella_copri    Simiaoa_sunii       Streptococcus_salivarius
##  Min.   :0.000000   Min.   :0.000e+00   Min.   :0.0000000       
##  1st Qu.:0.000000   1st Qu.:4.175e-05   1st Qu.:0.0000000       
##  Median :0.000000   Median :3.548e-04   Median :0.0000425       
##  Mean   :0.053750   Mean   :5.804e-03   Mean   :0.0002862       
##  3rd Qu.:0.002339   3rd Qu.:1.894e-03   3rd Qu.:0.0002217       
##  Max.   :0.875153   Max.   :1.305e-01   Max.   :0.0060953       
##  Streptococcus_thermophilus Sutterella_wadsworthensis Vescimonas_coprocola
##  Min.   :0.000e+00          Min.   :0.0000000         Min.   :0.000e+00   
##  1st Qu.:0.000e+00          1st Qu.:0.0000000         1st Qu.:5.225e-05   
##  Median :0.000e+00          Median :0.0005466         Median :3.524e-04   
##  Mean   :4.705e-04          Mean   :0.0080873         Mean   :1.540e-03   
##  3rd Qu.:8.098e-05          3rd Qu.:0.0078811         3rd Qu.:1.695e-03   
##  Max.   :1.331e-02          Max.   :0.1077498         Max.   :1.477e-02   
##  Wansuia_hejianensis Youxingia_wuxianensis bacterium_210917_DFI_7_65
##  Min.   :0.000e+00   Min.   :0.000e+00     Min.   :0.000e+00        
##  1st Qu.:0.000e+00   1st Qu.:0.000e+00     1st Qu.:0.000e+00        
##  Median :0.000e+00   Median :0.000e+00     Median :4.355e-05        
##  Mean   :8.419e-06   Mean   :1.314e-05     Mean   :1.739e-04        
##  3rd Qu.:4.950e-06   3rd Qu.:1.177e-05     3rd Qu.:2.004e-04        
##  Max.   :9.910e-05   Max.   :3.276e-04     Max.   :2.070e-03        
##  Bacteroides_faecis  Clostridiaceae_unclassified_SGB4771
##  Min.   :0.0000000   Min.   :0.000e+00                  
##  1st Qu.:0.0000000   1st Qu.:0.000e+00                  
##  Median :0.0000000   Median :2.550e-06                  
##  Mean   :0.0016892   Mean   :2.457e-04                  
##  3rd Qu.:0.0003732   3rd Qu.:2.629e-04                  
##  Max.   :0.0924332   Max.   :7.316e-03                  
##  Clostridium_sp_AM49_4BH Colidextribacter_sp_210702_DFI_3_9
##  Min.   :0.0000000       Min.   :0.000e+00                 
##  1st Qu.:0.0000000       1st Qu.:0.000e+00                 
##  Median :0.0000186       Median :0.000e+00                 
##  Mean   :0.0009479       Mean   :7.751e-05                 
##  3rd Qu.:0.0006711       3rd Qu.:8.565e-05                 
##  Max.   :0.0137412       Max.   :2.295e-03                 
##  Enterocloster_lavalensis GGB2982_SGB3964     GGB3304_SGB4367   
##  Min.   :0.000e+00        Min.   :0.0000000   Min.   :0.000000  
##  1st Qu.:0.000e+00        1st Qu.:0.0000000   1st Qu.:0.000000  
##  Median :0.000e+00        Median :0.0000000   Median :0.000000  
##  Mean   :3.657e-05        Mean   :0.0001603   Mean   :0.006249  
##  3rd Qu.:1.895e-05        3rd Qu.:0.0000758   3rd Qu.:0.004215  
##  Max.   :7.739e-04        Max.   :0.0062970   Max.   :0.074871  
##  GGB3619_SGB4894     GGB9296_SGB14253    GGB9524_SGB14924   
##  Min.   :0.0000000   Min.   :0.000e+00   Min.   :0.0000000  
##  1st Qu.:0.0000000   1st Qu.:0.000e+00   1st Qu.:0.0000000  
##  Median :0.0000000   Median :0.000e+00   Median :0.0000000  
##  Mean   :0.0004313   Mean   :1.571e-04   Mean   :0.0003030  
##  3rd Qu.:0.0000683   3rd Qu.:6.025e-05   3rd Qu.:0.0001647  
##  Max.   :0.0159758   Max.   :3.502e-03   Max.   :0.0143200  
##  GGB9574_SGB14987    GGB9619_SGB15066    GGB9707_SGB15229   
##  Min.   :0.000e+00   Min.   :0.000e+00   Min.   :0.0000000  
##  1st Qu.:0.000e+00   1st Qu.:0.000e+00   1st Qu.:0.0000000  
##  Median :0.000e+00   Median :0.000e+00   Median :0.0002587  
##  Mean   :3.523e-05   Mean   :9.250e-05   Mean   :0.0009222  
##  3rd Qu.:1.410e-05   3rd Qu.:4.750e-07   3rd Qu.:0.0010870  
##  Max.   :7.737e-04   Max.   :2.504e-03   Max.   :0.0138493  
##  GGB9708_SGB15233    GGB9760_SGB15374    Roseburia_sp_AF02_12
##  Min.   :0.0000000   Min.   :0.0000000   Min.   :0.0000000   
##  1st Qu.:0.0000000   1st Qu.:0.0000000   1st Qu.:0.0000000   
##  Median :0.0000000   Median :0.0000000   Median :0.0000331   
##  Mean   :0.0012046   Mean   :0.0005325   Mean   :0.0011198   
##  3rd Qu.:0.0003848   3rd Qu.:0.0005236   3rd Qu.:0.0004146   
##  Max.   :0.0814039   Max.   :0.0080872   Max.   :0.0369606   
##  Segatella_brunsvicensis Wujia_chipingensis  Alistipes_dispar   
##  Min.   :0.00000         Min.   :0.000e+00   Min.   :0.0000000  
##  1st Qu.:0.00000         1st Qu.:0.000e+00   1st Qu.:0.0000000  
##  Median :0.00000         Median :1.350e-06   Median :0.0000000  
##  Mean   :0.01194         Mean   :3.619e-03   Mean   :0.0006519  
##  3rd Qu.:0.00000         3rd Qu.:1.596e-03   3rd Qu.:0.0002937  
##  Max.   :0.49458         Max.   :5.839e-02   Max.   :0.0180946  
##  Alistipes_sp_AF17_16 Anaerobutyricum_soehngenii Anaerosacchariphilus_sp_NSJ_68
##  Min.   :0.000000     Min.   :0.000e+00          Min.   :0.000e+00             
##  1st Qu.:0.000000     1st Qu.:0.000e+00          1st Qu.:0.000e+00             
##  Median :0.000000     Median :0.000e+00          Median :0.000e+00             
##  Mean   :0.000748     Mean   :2.674e-04          Mean   :2.093e-05             
##  3rd Qu.:0.000610     3rd Qu.:5.907e-05          3rd Qu.:2.445e-05             
##  Max.   :0.025402     Max.   :1.237e-02          Max.   :4.210e-04             
##  Anaerotignum_sp_MSJ_24 Bittarella_massiliensis Blautia_SGB4815    
##  Min.   :0.000e+00      Min.   :0.000e+00       Min.   :0.000e+00  
##  1st Qu.:0.000e+00      1st Qu.:0.000e+00       1st Qu.:0.000e+00  
##  Median :0.000e+00      Median :0.000e+00       Median :1.865e-05  
##  Mean   :7.179e-05      Mean   :5.698e-06       Mean   :1.717e-04  
##  3rd Qu.:4.945e-05      3rd Qu.:0.000e+00       3rd Qu.:1.663e-04  
##  Max.   :1.074e-03      Max.   :1.359e-04       Max.   :2.406e-03  
##   Blautia_luti       Blautia_sp_OF03_15BH Butyricimonas_paravirosa
##  Min.   :0.000e+00   Min.   :0.000e+00    Min.   :0.000e+00       
##  1st Qu.:0.000e+00   1st Qu.:0.000e+00    1st Qu.:0.000e+00       
##  Median :2.500e-07   Median :0.000e+00    Median :0.000e+00       
##  Mean   :2.047e-04   Mean   :2.752e-05    Mean   :1.116e-04       
##  3rd Qu.:1.812e-04   3rd Qu.:7.575e-06    3rd Qu.:4.282e-05       
##  Max.   :3.159e-03   Max.   :5.829e-04    Max.   :2.880e-03       
##  Catenibacillus_scindens Clostridiaceae_bacterium_Marseille_Q4149
##  Min.   :0.000e+00       Min.   :0.000000                        
##  1st Qu.:0.000e+00       1st Qu.:0.000000                        
##  Median :0.000e+00       Median :0.000000                        
##  Mean   :2.672e-06       Mean   :0.002353                        
##  3rd Qu.:0.000e+00       3rd Qu.:0.000518                        
##  Max.   :1.314e-04       Max.   :0.071946                        
##  Clostridium_SGB6173 Clostridium_SGB6179 Clostridium_sp_Marseille_P3244
##  Min.   :0.0000000   Min.   :0.000e+00   Min.   :0.00e+00              
##  1st Qu.:0.0000000   1st Qu.:0.000e+00   1st Qu.:0.00e+00              
##  Median :0.0000000   Median :0.000e+00   Median :0.00e+00              
##  Mean   :0.0002150   Mean   :2.551e-04   Mean   :1.64e-06              
##  3rd Qu.:0.0000594   3rd Qu.:1.477e-05   3rd Qu.:0.00e+00              
##  Max.   :0.0070830   Max.   :1.128e-02   Max.   :4.92e-05              
##  Clostridium_sp_NSJ_42 Coprobacter_secundus Eubacteriaceae_bacterium
##  Min.   :0.0000000     Min.   :0.000e+00    Min.   :0.0000000       
##  1st Qu.:0.0000000     1st Qu.:0.000e+00    1st Qu.:0.0000000       
##  Median :0.0000000     Median :0.000e+00    Median :0.0000069       
##  Mean   :0.0002742     Mean   :5.297e-05    Mean   :0.0009817       
##  3rd Qu.:0.0000000     3rd Qu.:2.170e-05    3rd Qu.:0.0001183       
##  Max.   :0.0242940     Max.   :1.561e-03    Max.   :0.0525183       
##  Faecalibacillus_faecis Faecalibacillus_intestinalis GGB13489_SGB15224  
##  Min.   :0.000e+00      Min.   :0.0000000            Min.   :0.0000000  
##  1st Qu.:0.000e+00      1st Qu.:0.0000000            1st Qu.:0.0000000  
##  Median :0.000e+00      Median :0.0001854            Median :0.0000000  
##  Mean   :1.902e-04      Mean   :0.0010312            Mean   :0.0004354  
##  3rd Qu.:7.625e-06      3rd Qu.:0.0011422            3rd Qu.:0.0004191  
##  Max.   :6.796e-03      Max.   :0.0196735            Max.   :0.0052515  
##  GGB2970_SGB3952     GGB3352_SGB4436     GGB34797_SGB14322  
##  Min.   :0.0000000   Min.   :0.000e+00   Min.   :0.0000000  
##  1st Qu.:0.0000000   1st Qu.:0.000e+00   1st Qu.:0.0000000  
##  Median :0.0000000   Median :0.000e+00   Median :0.0000000  
##  Mean   :0.0001193   Mean   :1.587e-05   Mean   :0.0002539  
##  3rd Qu.:0.0000663   3rd Qu.:0.000e+00   3rd Qu.:0.0001889  
##  Max.   :0.0017474   Max.   :4.009e-04   Max.   :0.0054767  
##  GGB34900_SGB14891   GGB3653_SGB4964     GGB4456_SGB6141    
##  Min.   :0.000e+00   Min.   :0.0000000   Min.   :0.000e+00  
##  1st Qu.:0.000e+00   1st Qu.:0.0000000   1st Qu.:0.000e+00  
##  Median :0.000e+00   Median :0.0000007   Median :0.000e+00  
##  Mean   :8.752e-06   Mean   :0.0005639   Mean   :5.739e-05  
##  3rd Qu.:0.000e+00   3rd Qu.:0.0004370   3rd Qu.:0.000e+00  
##  Max.   :1.698e-04   Max.   :0.0092754   Max.   :1.605e-03  
##  GGB4552_SGB6276     GGB51441_SGB71759   GGB58158_SGB79798  
##  Min.   :0.0000000   Min.   :0.0000000   Min.   :0.000e+00  
##  1st Qu.:0.0000000   1st Qu.:0.0000000   1st Qu.:0.000e+00  
##  Median :0.0000000   Median :0.0000190   Median :0.000e+00  
##  Mean   :0.0016796   Mean   :0.0001130   Mean   :6.287e-06  
##  3rd Qu.:0.0005256   3rd Qu.:0.0001015   3rd Qu.:2.700e-06  
##  Max.   :0.0681626   Max.   :0.0023149   Max.   :2.230e-04  
##  GGB9365_SGB14341    GGB9412_SGB14770    GGB9627_SGB15081    GGB9712_SGB15244  
##  Min.   :0.000e+00   Min.   :0.0000000   Min.   :0.0000000   Min.   :0.000000  
##  1st Qu.:0.000e+00   1st Qu.:0.0000000   1st Qu.:0.0000000   1st Qu.:0.000000  
##  Median :0.000e+00   Median :0.0000000   Median :0.0000375   Median :0.000000  
##  Mean   :1.912e-04   Mean   :0.0002044   Mean   :0.0008485   Mean   :0.000957  
##  3rd Qu.:6.583e-05   3rd Qu.:0.0000000   3rd Qu.:0.0008041   3rd Qu.:0.000137  
##  Max.   :4.736e-03   Max.   :0.0091035   Max.   :0.0086268   Max.   :0.017285  
##  GGB9747_SGB15356   GGB9767_SGB15385    GGB9787_SGB15410    GGB9790_SGB15413   
##  Min.   :0.000000   Min.   :0.000e+00   Min.   :0.000e+00   Min.   :0.000e+00  
##  1st Qu.:0.000000   1st Qu.:0.000e+00   1st Qu.:0.000e+00   1st Qu.:0.000e+00  
##  Median :0.000000   Median :0.000e+00   Median :0.000e+00   Median :0.000e+00  
##  Mean   :0.002757   Mean   :1.957e-04   Mean   :4.775e-05   Mean   :4.165e-05  
##  3rd Qu.:0.001799   3rd Qu.:6.407e-05   3rd Qu.:2.465e-05   3rd Qu.:0.000e+00  
##  Max.   :0.038223   Max.   :5.067e-03   Max.   :7.156e-04   Max.   :6.338e-04  
##  Haemophilus_parainfluenzae Intestinibacter_bartlettii Lachnospira_sp_NSJ_43
##  Min.   :0.000e+00          Min.   :0.0000000          Min.   :0.000e+00    
##  1st Qu.:0.000e+00          1st Qu.:0.0000000          1st Qu.:0.000e+00    
##  Median :0.000e+00          Median :0.0000000          Median :3.465e-05    
##  Mean   :7.688e-05          Mean   :0.0001579          Mean   :2.091e-03    
##  3rd Qu.:6.148e-05          3rd Qu.:0.0000672          3rd Qu.:1.183e-03    
##  Max.   :1.461e-03          Max.   :0.0022551          Max.   :6.286e-02    
##  Lachnospiraceae_bacterium_OM04_12BH Lactococcus_lactis 
##  Min.   :0.000e+00                   Min.   :0.000e+00  
##  1st Qu.:0.000e+00                   1st Qu.:0.000e+00  
##  Median :0.000e+00                   Median :0.000e+00  
##  Mean   :1.669e-04                   Mean   :9.802e-05  
##  3rd Qu.:4.278e-05                   3rd Qu.:0.000e+00  
##  Max.   :6.780e-03                   Max.   :6.193e-03  
##  Lentihominibacter_faecis Massilioclostridium_coli
##  Min.   :0.000e+00        Min.   :0.000e+00       
##  1st Qu.:0.000e+00        1st Qu.:0.000e+00       
##  Median :4.500e-07        Median :0.000e+00       
##  Mean   :1.079e-04        Mean   :3.337e-05       
##  3rd Qu.:7.747e-05        3rd Qu.:4.450e-06       
##  Max.   :3.173e-03        Max.   :1.454e-03       
##  Mediterraneibacter_butyricigenes Mediterraneibacter_sp_NSJ_151
##  Min.   :0.000e+00                Min.   :0.000e+00            
##  1st Qu.:0.000e+00                1st Qu.:0.000e+00            
##  Median :2.600e-06                Median :0.000e+00            
##  Mean   :3.768e-05                Mean   :1.456e-05            
##  3rd Qu.:3.192e-05                3rd Qu.:0.000e+00            
##  Max.   :4.621e-04                Max.   :3.043e-04            
##  Methanobrevibacter_smithii Romboutsia_timonensis Ruminococcus_gnavus
##  Min.   :0.000000           Min.   :0.000e+00     Min.   :0.000e+00  
##  1st Qu.:0.000000           1st Qu.:0.000e+00     1st Qu.:0.000e+00  
##  Median :0.000000           Median :6.500e-07     Median :1.500e-07  
##  Mean   :0.001604           Mean   :4.635e-04     Mean   :1.062e-03  
##  3rd Qu.:0.000000           3rd Qu.:2.556e-04     3rd Qu.:1.167e-04  
##  Max.   :0.099630           Max.   :2.028e-02     Max.   :1.093e-01  
##  Ruminococcus_lactaris Ruminococcus_sp_AF41_9 Senegalimassilia_anaerobia
##  Min.   :0.000e+00     Min.   :0.0000000      Min.   :0.000e+00         
##  1st Qu.:0.000e+00     1st Qu.:0.0000000      1st Qu.:0.000e+00         
##  Median :3.785e-05     Median :0.0000000      Median :0.000e+00         
##  Mean   :6.396e-04     Mean   :0.0002778      Mean   :8.710e-05         
##  3rd Qu.:6.091e-04     3rd Qu.:0.0000736      3rd Qu.:5.245e-05         
##  Max.   :9.091e-03     Max.   :0.0091418      Max.   :1.817e-03         
##  Slackia_isoflavoniconvertens Streptococcus_parasanguinis Veillonella_dispar 
##  Min.   :0.0000000            Min.   :0.000e+00           Min.   :0.000e+00  
##  1st Qu.:0.0000000            1st Qu.:0.000e+00           1st Qu.:0.000e+00  
##  Median :0.0000000            Median :2.700e-06           Median :0.000e+00  
##  Mean   :0.0003184            Mean   :9.943e-05           Mean   :1.182e-04  
##  3rd Qu.:0.0002430            3rd Qu.:7.952e-05           3rd Qu.:7.177e-05  
##  Max.   :0.0084554            Max.   :1.600e-03           Max.   :2.388e-03  
##  Victivallis_lenta   Bifidobacterium_pseudocatenulatum Eubacterium_sp_AF34_35BH
##  Min.   :0.0000000   Min.   :0.000e+00                 Min.   :0.0000000       
##  1st Qu.:0.0000000   1st Qu.:0.000e+00                 1st Qu.:0.0000000       
##  Median :0.0000000   Median :0.000e+00                 Median :0.0000000       
##  Mean   :0.0003579   Mean   :5.605e-04                 Mean   :0.0001452       
##  3rd Qu.:0.0000000   3rd Qu.:3.013e-05                 3rd Qu.:0.0000919       
##  Max.   :0.0092131   Max.   :1.278e-02                 Max.   :0.0027871       
##  Faecalicatena_contorta GGB9559_SGB14969    GGB9759_SGB15370   
##  Min.   :0.000e+00      Min.   :0.000e+00   Min.   :0.0000000  
##  1st Qu.:0.000e+00      1st Qu.:0.000e+00   1st Qu.:0.0000000  
##  Median :0.000e+00      Median :0.000e+00   Median :0.0000000  
##  Mean   :1.262e-05      Mean   :5.645e-05   Mean   :0.0002567  
##  3rd Qu.:0.000e+00      3rd Qu.:5.060e-05   3rd Qu.:0.0002142  
##  Max.   :3.469e-04      Max.   :6.278e-04   Max.   :0.0054074  
##  Roseburia_lenta     Enterocloster_bolteae GGB2848_SGB3813    
##  Min.   :0.0000000   Min.   :0.0000000     Min.   :0.000e+00  
##  1st Qu.:0.0000000   1st Qu.:0.0000000     1st Qu.:0.000e+00  
##  Median :0.0000000   Median :0.0000030     Median :0.000e+00  
##  Mean   :0.0012327   Mean   :0.0001893     Mean   :3.600e-05  
##  3rd Qu.:0.0003235   3rd Qu.:0.0001183     3rd Qu.:2.275e-05  
##  Max.   :0.0412711   Max.   :0.0036707     Max.   :1.635e-03  
##  GGB3005_SGB3996     GGB3061_SGB4063     GGB36331_SGB15121  
##  Min.   :0.000e+00   Min.   :0.000e+00   Min.   :0.0000000  
##  1st Qu.:0.000e+00   1st Qu.:0.000e+00   1st Qu.:0.0000000  
##  Median :0.000e+00   Median :0.000e+00   Median :0.0000000  
##  Mean   :4.229e-05   Mean   :4.684e-05   Mean   :0.0001415  
##  3rd Qu.:2.050e-06   3rd Qu.:2.175e-06   3rd Qu.:0.0000797  
##  Max.   :2.103e-03   Max.   :1.154e-03   Max.   :0.0021450  
##  Hungatella_hathewayi TM7_phylum_sp_oral_taxon_352 Veillonella_parvula
##  Min.   :0.000e+00    Min.   :0.0000000            Min.   :0.000e+00  
##  1st Qu.:0.000e+00    1st Qu.:0.0000000            1st Qu.:0.000e+00  
##  Median :0.000e+00    Median :0.0000000            Median :0.000e+00  
##  Mean   :1.890e-04    Mean   :0.0000476            Mean   :2.101e-04  
##  3rd Qu.:9.750e-06    3rd Qu.:0.0000476            3rd Qu.:6.352e-05  
##  Max.   :2.653e-02    Max.   :0.0011388            Max.   :9.409e-03  
##  GGB6649_SGB9391     Veillonella_atypica
##  Min.   :0.0000000   Min.   :0.000e+00  
##  1st Qu.:0.0000000   1st Qu.:0.000e+00  
##  Median :0.0000000   Median :0.000e+00  
##  Mean   :0.0002582   Mean   :9.890e-05  
##  3rd Qu.:0.0003208   3rd Qu.:2.483e-05  
##  Max.   :0.0031719   Max.   :2.649e-03

data_microbiome_original_raw[1:15, 1:5]
##    Sample Country  Diet Adlercreutzia_equolifaciens
## 1     T36      CZ VEGAN                   0.0000155
## 2     T47      CZ VEGAN                   0.0000220
## 3     T55      CZ VEGAN                   0.0000103
## 4     T59      CZ VEGAN                   0.0000000
## 5     T60      CZ VEGAN                   0.0000103
## 6     T61      CZ VEGAN                   0.0000000
## 7     T66      CZ VEGAN                   0.0000812
## 8     T67      CZ VEGAN                   0.0009972
## 9     T68      CZ VEGAN                   0.0000146
## 10    T69      CZ VEGAN                   0.0002147
## 11    T70      CZ VEGAN                   0.0000486
## 12    T71      CZ VEGAN                   0.0000000
## 13    T72      CZ VEGAN                   0.0000752
## 14    T85      CZ VEGAN                   0.0006369
## 15    T86      CZ VEGAN                   0.0000000
##    Agathobaculum_butyriciproducens
## 1                        0.0001334
## 2                        0.0066116
## 3                        0.0027177
## 4                        0.0013599
## 5                        0.0010438
## 6                        0.0108596
## 7                        0.0018825
## 8                        0.0078466
## 9                        0.0058316
## 10                       0.0101227
## 11                       0.0005179
## 12                       0.0063437
## 13                       0.0039945
## 14                       0.0069611
## 15                       0.0014984

3.1.2 Validation set

3.1.2.1 Get metadata from lipidom table

Open code
data_lipids_validation <- read.xlsx('gitignore/data/lipidome_validation_cohort.xlsx') %>% 
  select(X1, X2) %>% 
  mutate(ID = X1)

3.1.2.2 Connect validation data

Open code
data_microbiome_validation_raw <- read.table(
  'gitignore/data/0_Data_Metaphlan4_species_filtered_KOMPAS_rel_ab.txt') %>% t()

colnames(data_microbiome_validation_raw) <- data_microbiome_validation_raw[1,]

data_microbiome_validation_raw <- data_microbiome_validation_raw[-1, ] %>% data.frame() %>%
  mutate(
    ID = paste0("K", gsub("\\..*", "", trimws(ID))),
    across(Adlercreutzia_equolifaciens:Veillonella_atypica, ~ as.numeric(.)/100)
  ) %>% 
  left_join(data_lipids_validation, by = 'ID') %>% 
  mutate(Data = 'valid', Sample = ID, Diet = X2) %>% 
  select(Sample, Data, Diet, everything()) %>% 
  select(-ID, -X1, -X2)

3.1.3 Get center-log transformed value

Open code
## Training data
metadata <- data_microbiome_original_raw[, c("Sample", "Country", "Diet")]
bacteria_data <- data_microbiome_original_raw[, -(1:3)]
clr_bacteria_data <- clr(bacteria_data)
data_microbiome_original <- cbind(metadata, clr_bacteria_data)

## Validation data
metadata <- data_microbiome_validation_raw[, c("Sample", "Data", "Diet")]
bacteria_data <- data_microbiome_validation_raw[, -(1:3)]
clr_bacteria_data <- clr(bacteria_data)
data_microbiome_validation <- cbind(metadata, clr_bacteria_data)

3.1.4 Merge training and validation dataset

Open code
common_microbiome <- intersect(
  colnames(data_microbiome_original), 
  colnames(data_microbiome_validation))[-c(1:2)]

tr1 <- data_microbiome_original %>% 
  mutate(Data = if_else(Country == 'CZ', 'CZ_tr', 'IT_tr')) %>% 
  select(Data, Diet, all_of(common_microbiome))

tr2 <- data_microbiome_validation %>% 
  mutate(Data = 'valid',
         Diet = Diet) %>% 
  select(Data, Diet, all_of(common_microbiome))

data_merged <- bind_rows(tr1, tr2)

3.2 Explore

3.2.1 Data summary

Open code
summary(data_microbiome_original)
##     Sample            Country              Diet          
##  Length:166         Length:166         Length:166        
##  Class :character   Class :character   Class :character  
##  Mode  :character   Mode  :character   Mode  :character  
##                                                          
##                                                          
##                                                          
##  Adlercreutzia_equolifaciens Agathobaculum_butyriciproducens
##  Min.   :-5.3879             Min.   :-1.6741                
##  1st Qu.:-1.8236             1st Qu.: 0.9966                
##  Median :-0.3954             Median : 1.7080                
##  Mean   :-0.9361             Mean   : 1.6332                
##  3rd Qu.: 0.0000             3rd Qu.: 2.3623                
##  Max.   : 2.9097             Max.   : 4.1360                
##  Akkermansia_muciniphila Alistipes_communis Alistipes_finegoldii
##  Min.   :-5.961          Min.   :-4.579     Min.   :-5.9534     
##  1st Qu.: 0.000          1st Qu.: 0.000     1st Qu.: 0.0000     
##  Median : 1.018          Median : 1.911     Median : 0.4529     
##  Mean   : 1.437          Mean   : 1.666     Mean   : 0.8876     
##  3rd Qu.: 3.155          3rd Qu.: 2.925     3rd Qu.: 2.0030     
##  Max.   : 7.112          Max.   : 5.808     Max.   : 5.2364     
##  Alistipes_ihumii  Alistipes_indistinctus Alistipes_onderdonkii
##  Min.   :-4.4586   Min.   :-5.34668       Min.   :-5.68594     
##  1st Qu.: 0.0000   1st Qu.:-0.46130       1st Qu.: 0.02463     
##  Median : 0.1777   Median : 0.00000       Median : 2.08366     
##  Mean   : 0.8382   Mean   :-0.05192       Mean   : 1.83492     
##  3rd Qu.: 1.8759   3rd Qu.: 0.60784       3rd Qu.: 3.50525     
##  Max.   : 4.4281   Max.   : 3.54569       Max.   : 6.75375     
##  Alistipes_putredinis Alistipes_senegalensis Alistipes_shahii
##  Min.   :-7.606       Min.   :-5.4138        Min.   :-6.235  
##  1st Qu.: 1.605       1st Qu.: 0.0000        1st Qu.: 0.917  
##  Median : 3.783       Median : 0.0000        Median : 2.579  
##  Mean   : 2.960       Mean   : 0.2239        Mean   : 2.249  
##  3rd Qu.: 4.945       3rd Qu.: 0.7422        3rd Qu.: 3.601  
##  Max.   : 6.531       Max.   : 4.9916        Max.   : 5.574  
##  Anaerobutyricum_hallii Anaerofilum_hominis Anaeromassilibacillus_senegalensis
##  Min.   :-6.53505       Min.   :-6.448      Min.   :-6.027                    
##  1st Qu.:-0.53293       1st Qu.:-2.698      1st Qu.:-2.005                    
##  Median : 0.00000       Median : 0.000      Median :-0.154                    
##  Mean   :-0.04001       Mean   :-1.190      Mean   :-1.108                    
##  3rd Qu.: 1.03361       3rd Qu.: 0.000      3rd Qu.: 0.000                    
##  Max.   : 2.70957       Max.   : 1.493      Max.   : 2.877                    
##  Anaerostipes_hadrus Anaerotignum_faecicola Anaerotruncus_colihominis
##  Min.   :-6.0832     Min.   :-5.55638       Min.   :-5.1760          
##  1st Qu.:-0.2503     1st Qu.:-0.02553       1st Qu.:-1.2463          
##  Median : 0.7114     Median : 0.00000       Median : 0.0000          
##  Mean   : 0.5021     Mean   : 0.31693       Mean   :-0.7356          
##  3rd Qu.: 1.9325     3rd Qu.: 1.12255       3rd Qu.: 0.0000          
##  Max.   : 4.6126     Max.   : 3.53207       Max.   : 1.8766          
##  Anaerotruncus_massiliensis Anaerotruncus_rubiinfantis Bacteroides_caccae
##  Min.   :-5.8087            Min.   :-6.8486            Min.   :-7.0322   
##  1st Qu.: 0.0000            1st Qu.:-1.8683            1st Qu.: 0.0000   
##  Median : 0.0000            Median :-0.3007            Median : 0.7947   
##  Mean   :-0.5276            Mean   :-1.0680            Mean   : 1.1023   
##  3rd Qu.: 0.0000            3rd Qu.: 0.0000            3rd Qu.: 2.3678   
##  Max.   : 1.8737            Max.   : 0.4163            Max.   : 5.5946   
##  Bacteroides_cellulosilyticus Bacteroides_clarus Bacteroides_eggerthii
##  Min.   :-6.5276              Min.   :-5.87834   Min.   :-5.8104      
##  1st Qu.: 0.0000              1st Qu.: 0.00000   1st Qu.: 0.0000      
##  Median : 0.0000              Median : 0.00000   Median : 0.0000      
##  Mean   : 0.3400              Mean   : 0.02645   Mean   : 0.1948      
##  3rd Qu.: 0.7151              3rd Qu.: 0.00000   3rd Qu.: 0.7557      
##  Max.   : 5.5202              Max.   : 5.54521   Max.   : 5.1987      
##  Bacteroides_fragilis Bacteroides_ovatus Bacteroides_stercoris
##  Min.   :-4.1363      Min.   :-4.48695   Min.   :-5.6643      
##  1st Qu.: 0.0000      1st Qu.: 0.08505   1st Qu.: 0.0000      
##  Median : 0.0000      Median : 1.49041   Median : 0.0000      
##  Mean   : 0.1575      Mean   : 1.38139   Mean   : 0.7809      
##  3rd Qu.: 0.0000      3rd Qu.: 2.77379   3rd Qu.: 2.3743      
##  Max.   : 4.2877      Max.   : 5.60476   Max.   : 5.8632      
##  Bacteroides_thetaiotaomicron Bacteroides_uniformis Bacteroides_xylanisolvens
##  Min.   :-5.9862              Min.   :-4.205        Min.   :-4.4018          
##  1st Qu.:-0.4044              1st Qu.: 2.439        1st Qu.:-0.4428          
##  Median : 0.3483              Median : 3.601        Median : 0.0000          
##  Mean   : 0.3787              Mean   : 3.421        Mean   : 0.2817          
##  3rd Qu.: 1.7410              3rd Qu.: 4.620        3rd Qu.: 1.2479          
##  Max.   : 4.6917              Max.   : 6.136        Max.   : 4.9017          
##  Barnesiella_intestinihominis Bifidobacterium_adolescentis
##  Min.   :-4.622               Min.   :-5.687              
##  1st Qu.: 0.000               1st Qu.: 0.000              
##  Median : 1.149               Median : 1.780              
##  Mean   : 1.137               Mean   : 1.413              
##  3rd Qu.: 2.178               3rd Qu.: 3.042              
##  Max.   : 4.642               Max.   : 5.701              
##  Bifidobacterium_longum Bilophila_SGB15451 Bilophila_wadsworthia
##  Min.   :-4.802         Min.   :-5.0800    Min.   :-5.3209      
##  1st Qu.: 0.000         1st Qu.: 0.0000    1st Qu.:-0.2692      
##  Median : 1.278         Median : 0.0000    Median : 0.4433      
##  Mean   : 1.261         Mean   :-0.2986    Mean   : 0.4978      
##  3rd Qu.: 2.186         3rd Qu.: 0.0000    3rd Qu.: 1.5429      
##  Max.   : 6.492         Max.   : 2.8823    Max.   : 4.0864      
##  Blautia_faecis     Blautia_glucerasea Blautia_massiliensis Blautia_obeum    
##  Min.   :-4.88005   Min.   :-6.4562    Min.   :-7.3557      Min.   :-5.2312  
##  1st Qu.:-0.83153   1st Qu.:-1.1658    1st Qu.:-0.6892      1st Qu.:-1.0399  
##  Median : 0.00000   Median : 0.0000    Median : 0.0000      Median : 0.0000  
##  Mean   :-0.08774   Mean   :-0.5844    Mean   :-0.1389      Mean   :-0.2131  
##  3rd Qu.: 0.87471   3rd Qu.: 0.2766    3rd Qu.: 0.8917      3rd Qu.: 0.6754  
##  Max.   : 4.39225   Max.   : 2.6244    Max.   : 4.3965      Max.   : 3.6839  
##  Blautia_sp_MCC283 Blautia_wexlerae  Brotolimicola_acetigignens
##  Min.   :-5.6218   Min.   :-5.8602   Min.   :-3.716            
##  1st Qu.:-1.0715   1st Qu.:-0.4109   1st Qu.: 0.000            
##  Median : 0.0000   Median : 1.1615   Median : 1.153            
##  Mean   :-0.2482   Mean   : 0.7826   Mean   : 1.206            
##  3rd Qu.: 0.4179   3rd Qu.: 2.1478   3rd Qu.: 2.560            
##  Max.   : 3.7660   Max.   : 4.9687   Max.   : 5.090            
##  Butyricimonas_faecihominis Butyricimonas_virosa
##  Min.   :-5.1290            Min.   :-5.8793     
##  1st Qu.:-0.4997            1st Qu.:-0.7518     
##  Median : 0.0000            Median : 0.0000     
##  Mean   :-0.3321            Mean   :-0.5573     
##  3rd Qu.: 0.0000            3rd Qu.: 0.0000     
##  Max.   : 2.2716            Max.   : 1.6800     
##  Candidatus_Borkfalkia_ceftriaxoniphila Candidatus_Cibionibacter_quicibialis
##  Min.   :-5.7494                        Min.   :-2.997                      
##  1st Qu.: 0.0000                        1st Qu.: 1.750                      
##  Median : 0.0000                        Median : 2.884                      
##  Mean   :-0.1109                        Mean   : 2.828                      
##  3rd Qu.: 0.0000                        3rd Qu.: 4.004                      
##  Max.   : 2.8325                        Max.   : 6.222                      
##  Clostridia_bacterium_UC5_1_1D1 Clostridiaceae_bacterium
##  Min.   :-5.4364                Min.   :-4.788408       
##  1st Qu.:-2.3233                1st Qu.:-0.000219       
##  Median :-0.4205                Median : 1.075284       
##  Mean   :-1.1843                Mean   : 0.759460       
##  3rd Qu.: 0.0000                3rd Qu.: 1.911031       
##  Max.   : 0.5711                Max.   : 3.368168       
##  Clostridiaceae_bacterium_AF18_31LB Clostridiaceae_bacterium_Marseille_Q4143
##  Min.   :-5.8178                    Min.   :-6.4472                         
##  1st Qu.:-1.1227                    1st Qu.:-1.9792                         
##  Median :-0.1195                    Median :-0.6454                         
##  Mean   :-0.4046                    Mean   :-1.0371                         
##  3rd Qu.: 0.2689                    3rd Qu.: 0.0000                         
##  Max.   : 2.9192                    Max.   : 1.4063                         
##  Clostridiaceae_bacterium_Marseille_Q4145 Clostridiales_bacterium
##  Min.   :-6.1207                          Min.   :-4.63910       
##  1st Qu.:-1.8869                          1st Qu.:-0.92139       
##  Median :-0.7634                          Median : 0.00000       
##  Mean   :-1.1618                          Mean   : 0.02174       
##  3rd Qu.: 0.0000                          3rd Qu.: 1.00087       
##  Max.   : 0.6652                          Max.   : 4.09011       
##  Clostridiales_bacterium_KLE1615 Clostridium_SGB4750 Clostridium_SGB4909
##  Min.   :-4.9682                 Min.   :-5.0596     Min.   :-5.7795    
##  1st Qu.:-0.4299                 1st Qu.:-1.5247     1st Qu.:-0.6520    
##  Median : 0.2944                 Median : 0.0000     Median : 0.0000    
##  Mean   : 0.1387                 Mean   :-0.5647     Mean   :-0.4153    
##  3rd Qu.: 1.1507                 3rd Qu.: 0.1326     3rd Qu.: 0.0000    
##  Max.   : 3.0587                 Max.   : 3.3859     Max.   : 4.0898    
##  Clostridium_fessum Clostridium_leptum Clostridium_sp_AF20_17LB
##  Min.   :-5.976     Min.   :-5.2099    Min.   :-5.45520        
##  1st Qu.: 0.565     1st Qu.:-2.0180    1st Qu.:-0.50576        
##  Median : 1.418     Median :-0.4343    Median : 0.00000        
##  Mean   : 1.307     Mean   :-0.9416    Mean   : 0.03637        
##  3rd Qu.: 2.094     3rd Qu.: 0.0000    3rd Qu.: 1.19653        
##  Max.   : 4.349     Max.   : 3.3064    Max.   : 3.09209        
##  Clostridium_sp_AF27_2AA Clostridium_sp_AF36_4 Clostridium_sp_AM22_11AC
##  Min.   :-4.5182         Min.   :-6.1933       Min.   :-3.6428         
##  1st Qu.:-0.8515         1st Qu.:-0.2940       1st Qu.:-0.3825         
##  Median : 0.0000         Median : 0.0000       Median : 0.4232         
##  Mean   :-0.2568         Mean   : 0.3057       Mean   : 0.4568         
##  3rd Qu.: 0.2150         3rd Qu.: 1.4536       3rd Qu.: 1.4361         
##  Max.   : 2.7417         Max.   : 4.7043       Max.   : 3.3216         
##  Clostridium_sp_AM33_3 Collinsella_aerofaciens Coprobacter_fastidiosus
##  Min.   :-4.06890      Min.   :-1.8321         Min.   :-6.0734        
##  1st Qu.:-0.40458      1st Qu.: 0.0000         1st Qu.:-0.6383        
##  Median : 0.00000      Median : 0.8381         Median : 0.0000        
##  Mean   :-0.01868      Mean   : 0.8620         Mean   :-0.5113        
##  3rd Qu.: 0.56758      3rd Qu.: 1.6157         3rd Qu.: 0.0000        
##  Max.   : 2.86121      Max.   : 3.9768         Max.   : 2.5060        
##  Coprococcus_catus Coprococcus_comes Coprococcus_eutactus Dorea_formicigenerans
##  Min.   :-5.1965   Min.   :-5.2215   Min.   :-6.1262      Min.   :-5.6458      
##  1st Qu.:-0.8594   1st Qu.:-0.6394   1st Qu.: 0.0000      1st Qu.:-1.1649      
##  Median : 0.0000   Median : 0.0000   Median : 0.9813      Median : 0.0000      
##  Mean   :-0.3717   Mean   :-0.1285   Mean   : 1.2233      Mean   :-0.5043      
##  3rd Qu.: 0.3124   3rd Qu.: 0.6050   3rd Qu.: 2.4333      3rd Qu.: 0.2688      
##  Max.   : 2.4296   Max.   : 3.2415   Max.   : 6.0710      Max.   : 2.0020      
##  Dorea_longicatena Dorea_sp_AF36_15AT Dysosmobacter_SGB15077
##  Min.   :-4.9302   Min.   :-6.7063    Min.   :-6.4363       
##  1st Qu.:-0.6733   1st Qu.:-2.0437    1st Qu.: 0.0000       
##  Median : 0.2830   Median :-0.7004    Median : 0.0000       
##  Mean   : 0.1425   Mean   :-1.1400    Mean   :-0.4436       
##  3rd Qu.: 1.3986   3rd Qu.: 0.0000    3rd Qu.: 0.0000       
##  Max.   : 3.3803   Max.   : 0.9716    Max.   : 3.8869       
##  Dysosmobacter_welbionis Eggerthella_lenta Enterocloster_citroniae
##  Min.   :-4.0071         Min.   :-6.4774   Min.   :-6.0016        
##  1st Qu.: 0.0000         1st Qu.:-1.2018   1st Qu.:-1.8957        
##  Median : 0.9038         Median : 0.0000   Median :-0.8421        
##  Mean   : 0.9727         Mean   :-0.8392   Mean   :-1.1850        
##  3rd Qu.: 2.3094         3rd Qu.: 0.0000   3rd Qu.: 0.0000        
##  Max.   : 5.0330         Max.   : 1.4281   Max.   : 0.7546        
##  Enterocloster_hominis Escherichia_coli  Eubacterium_ramulus
##  Min.   :-4.60696      Min.   :-4.9322   Min.   :-6.2096    
##  1st Qu.: 0.00000      1st Qu.:-1.1396   1st Qu.:-1.4087    
##  Median : 0.00000      Median : 0.0000   Median :-0.3327    
##  Mean   :-0.09605      Mean   :-0.1907   Mean   :-0.7996    
##  3rd Qu.: 0.00000      3rd Qu.: 0.5415   3rd Qu.: 0.0000    
##  Max.   : 3.59139      Max.   : 4.6124   Max.   : 1.7837    
##  Eubacterium_rectale Eubacterium_siraeum Eubacterium_ventriosum
##  Min.   :-6.790      Min.   :-6.4360     Min.   :-5.5382       
##  1st Qu.: 1.227      1st Qu.:-0.2593     1st Qu.:-1.0211       
##  Median : 2.596      Median : 0.0000     Median : 0.0000       
##  Mean   : 2.240      Mean   :-0.1503     Mean   :-0.3966       
##  3rd Qu.: 3.648      3rd Qu.: 0.0000     3rd Qu.: 0.3953       
##  Max.   : 5.434      Max.   : 4.4675     Max.   : 2.7794       
##  Faecalibacterium_SGB15346 Faecalibacterium_prausnitzii
##  Min.   :-6.1955           Min.   :-4.639              
##  1st Qu.: 0.3215           1st Qu.: 3.844              
##  Median : 1.8232           Median : 4.481              
##  Mean   : 1.5416           Mean   : 4.471              
##  3rd Qu.: 3.2713           3rd Qu.: 5.338              
##  Max.   : 5.7360           Max.   : 6.786              
##  Faecalibacterium_sp_CLA_AA_H233 Faecalibacterium_sp_HTFF
##  Min.   :-5.8488                 Min.   :-6.3530         
##  1st Qu.:-0.9810                 1st Qu.:-0.2376         
##  Median : 0.0000                 Median : 0.0000         
##  Mean   : 0.0375                 Mean   : 0.0274         
##  3rd Qu.: 1.3638                 3rd Qu.: 0.9419         
##  Max.   : 5.2997                 Max.   : 4.2136         
##  Faecalicatena_fissicatena Flavonifractor_plautii
##  Min.   :-5.3392           Min.   :-5.1080       
##  1st Qu.:-0.2981           1st Qu.:-1.1648       
##  Median : 0.0000           Median : 0.0000       
##  Mean   : 0.1068           Mean   :-0.1363       
##  3rd Qu.: 0.9194           3rd Qu.: 1.0215       
##  Max.   : 3.1942           Max.   : 3.2732       
##  Fusicatenibacter_saccharivorans Fusicatenibacter_sp_CLA_AA_H277
##  Min.   :-7.102                  Min.   :-4.6991                
##  1st Qu.: 1.090                  1st Qu.:-1.2460                
##  Median : 1.820                  Median :-0.1455                
##  Mean   : 1.677                  Mean   :-0.4842                
##  3rd Qu.: 2.438                  3rd Qu.: 0.2713                
##  Max.   : 4.882                  Max.   : 2.3209                
##  GGB13404_SGB14252 GGB1420_SGB1957    GGB2653_SGB3574   GGB2998_SGB3988  
##  Min.   :-5.9397   Min.   :-4.53110   Min.   :-6.5200   Min.   :-5.1524  
##  1st Qu.:-0.7179   1st Qu.: 0.00000   1st Qu.:-1.7597   1st Qu.:-1.1401  
##  Median : 0.0000   Median : 0.00000   Median :-0.4100   Median : 0.0000  
##  Mean   :-0.5002   Mean   : 0.03005   Mean   :-0.9612   Mean   :-0.5979  
##  3rd Qu.: 0.0000   3rd Qu.: 0.00000   3rd Qu.: 0.0000   3rd Qu.: 0.0000  
##  Max.   : 2.0974   Max.   : 2.98099   Max.   : 2.0777   Max.   : 1.9321  
##  GGB3034_SGB4030   GGB3109_SGB4121   GGB3175_SGB4191   GGB33469_SGB15236
##  Min.   :-5.6446   Min.   :-4.6465   Min.   :-4.7615   Min.   :-6.2739  
##  1st Qu.: 0.0000   1st Qu.:-0.7139   1st Qu.: 0.0000   1st Qu.: 0.0000  
##  Median : 0.0000   Median : 0.0000   Median : 0.0000   Median : 0.0000  
##  Mean   :-0.5141   Mean   :-0.3088   Mean   : 0.4437   Mean   : 0.2968  
##  3rd Qu.: 0.0000   3rd Qu.: 0.0000   3rd Qu.: 0.1534   3rd Qu.: 1.1847  
##  Max.   : 0.0000   Max.   : 2.4504   Max.   : 5.1548   Max.   : 5.4452  
##  GGB33512_SGB15203 GGB33586_SGB53517 GGB3537_SGB4727   GGB38744_SGB14842
##  Min.   :-3.856    Min.   :-4.2678   Min.   :-5.4365   Min.   :-5.8953  
##  1st Qu.: 0.000    1st Qu.:-0.4349   1st Qu.:-1.1792   1st Qu.: 0.0000  
##  Median : 0.000    Median : 0.0000   Median : 0.0000   Median : 0.0000  
##  Mean   :-0.124    Mean   :-0.3506   Mean   :-0.6529   Mean   :-0.6669  
##  3rd Qu.: 0.000    3rd Qu.: 0.0000   3rd Qu.: 0.0000   3rd Qu.: 0.0000  
##  Max.   : 4.904    Max.   : 2.7969   Max.   : 0.9486   Max.   : 0.0000  
##  GGB45432_SGB63101 GGB45613_SGB63326 GGB47687_SGB2286  GGB52106_SGB72838
##  Min.   :-5.6970   Min.   :-6.593    Min.   :-5.8572   Min.   :-4.7965  
##  1st Qu.:-2.4242   1st Qu.:-2.669    1st Qu.: 0.0000   1st Qu.:-0.5314  
##  Median :-0.5422   Median : 0.000    Median : 0.0000   Median : 0.0000  
##  Mean   :-1.2638   Mean   :-1.193    Mean   : 0.5912   Mean   :-0.5016  
##  3rd Qu.: 0.0000   3rd Qu.: 0.000    3rd Qu.: 0.8481   3rd Qu.: 0.0000  
##  Max.   : 0.3327   Max.   : 0.000    Max.   : 6.1121   Max.   : 1.3288  
##  GGB52130_SGB14966 GGB9062_SGB13981  GGB9063_SGB13982   GGB9064_SGB13983  
##  Min.   :-4.5439   Min.   :-5.4098   Min.   :-3.34675   Min.   :-4.67933  
##  1st Qu.:-1.2764   1st Qu.: 0.0000   1st Qu.: 0.00000   1st Qu.: 0.00000  
##  Median : 0.0000   Median : 0.0000   Median : 0.00000   Median : 0.00000  
##  Mean   :-0.6277   Mean   :-0.2607   Mean   : 0.04859   Mean   :-0.04388  
##  3rd Qu.: 0.0000   3rd Qu.: 0.0000   3rd Qu.: 0.00000   3rd Qu.: 0.00000  
##  Max.   : 1.6962   Max.   : 2.2215   Max.   : 4.07597   Max.   : 3.90533  
##  GGB9342_SGB14306  GGB9345_SGB14311  GGB9453_SGB14844  GGB9502_SGB14899  
##  Min.   :-5.6136   Min.   :-6.6626   Min.   :-5.3761   Min.   :-4.40294  
##  1st Qu.: 0.0000   1st Qu.: 0.0000   1st Qu.: 0.0000   1st Qu.: 0.00000  
##  Median : 0.0000   Median : 0.0000   Median : 0.0000   Median : 0.00000  
##  Mean   : 0.3031   Mean   : 0.4204   Mean   :-0.4094   Mean   : 0.01852  
##  3rd Qu.: 1.0113   3rd Qu.: 0.8474   3rd Qu.: 0.0000   3rd Qu.: 0.01587  
##  Max.   : 4.7917   Max.   : 4.8035   Max.   : 4.1317   Max.   : 2.52621  
##  GGB9509_SGB14906   GGB9522_SGB14921  GGB9531_SGB14932  GGB9534_SGB14937 
##  Min.   :-5.20406   Min.   :-4.7720   Min.   :-4.8496   Min.   :-6.1275  
##  1st Qu.: 0.00000   1st Qu.:-1.2779   1st Qu.:-0.1129   1st Qu.:-1.2666  
##  Median : 0.00000   Median : 0.0000   Median : 0.0000   Median : 0.0000  
##  Mean   : 0.05643   Mean   :-0.6737   Mean   :-0.3279   Mean   :-0.5408  
##  3rd Qu.: 0.00000   3rd Qu.: 0.0000   3rd Qu.: 0.0000   3rd Qu.: 0.0000  
##  Max.   : 4.75064   Max.   : 2.2978   Max.   : 1.8710   Max.   : 3.6275  
##  GGB9602_SGB15031  GGB9614_SGB15049  GGB9619_SGB15067  GGB9621_SGB15073   
##  Min.   :-5.0226   Min.   :-5.6756   Min.   :-4.9466   Min.   :-3.731002  
##  1st Qu.: 0.0000   1st Qu.:-0.2012   1st Qu.:-0.3116   1st Qu.: 0.000000  
##  Median : 0.0000   Median : 0.0000   Median : 0.0000   Median : 0.000000  
##  Mean   : 0.5927   Mean   : 0.2718   Mean   :-0.3647   Mean   :-0.006089  
##  3rd Qu.: 1.3147   3rd Qu.: 1.2096   3rd Qu.: 0.0000   3rd Qu.: 0.028730  
##  Max.   : 5.6397   Max.   : 3.3567   Max.   : 2.3513   Max.   : 2.402629  
##  GGB9635_SGB15106 GGB9646_SGB15123  GGB9667_SGB15164  GGB9699_SGB15216 
##  Min.   :-4.256   Min.   :-5.3458   Min.   :-5.5620   Min.   :-5.9559  
##  1st Qu.: 0.000   1st Qu.:-1.5106   1st Qu.:-0.3300   1st Qu.:-0.5640  
##  Median : 0.000   Median : 0.0000   Median : 0.0000   Median : 0.0000  
##  Mean   : 1.358   Mean   :-0.8929   Mean   :-0.1921   Mean   : 0.3048  
##  3rd Qu.: 3.116   3rd Qu.: 0.0000   3rd Qu.: 0.0153   3rd Qu.: 1.5112  
##  Max.   : 6.405   Max.   : 2.0239   Max.   : 3.0430   Max.   : 4.1608  
##  GGB9708_SGB15234  GGB9715_SGB15265 GGB9719_SGB15272  GGB9719_SGB15273 
##  Min.   :-6.1955   Min.   :-4.808   Min.   :-4.2084   Min.   :-4.0738  
##  1st Qu.: 0.0000   1st Qu.: 0.000   1st Qu.:-0.9183   1st Qu.: 0.0000  
##  Median : 0.0000   Median : 0.000   Median : 0.0000   Median : 0.0000  
##  Mean   : 0.6971   Mean   : 1.080   Mean   :-0.4853   Mean   :-0.3027  
##  3rd Qu.: 1.9222   3rd Qu.: 2.875   3rd Qu.: 0.0000   3rd Qu.: 0.0000  
##  Max.   : 5.5223   Max.   : 5.683   Max.   : 2.4982   Max.   : 1.6065  
##  GGB9730_SGB15291   GGB9758_SGB15368 GGB9760_SGB15373  GGB9765_SGB15382 
##  Min.   :-3.29380   Min.   :-6.406   Min.   :-3.4466   Min.   :-5.2182  
##  1st Qu.:-0.08604   1st Qu.: 0.000   1st Qu.:-0.2374   1st Qu.:-0.1042  
##  Median : 0.10778   Median : 1.351   Median : 0.0000   Median : 0.0000  
##  Mean   : 0.48088   Mean   : 1.804   Mean   : 0.2687   Mean   :-0.5102  
##  3rd Qu.: 1.41027   3rd Qu.: 4.179   3rd Qu.: 0.8841   3rd Qu.: 0.0000  
##  Max.   : 3.79637   Max.   : 7.262   Max.   : 3.6974   Max.   : 2.0323  
##  GGB9770_SGB15390  GGB9775_SGB15395   GGB9781_SGB15402  GGB9818_SGB15459 
##  Min.   :-5.7452   Min.   :-4.87045   Min.   :-5.6270   Min.   :-6.3782  
##  1st Qu.: 0.0000   1st Qu.: 0.00000   1st Qu.:-0.2432   1st Qu.: 0.0000  
##  Median : 0.0000   Median : 0.00000   Median : 0.0000   Median : 0.0000  
##  Mean   :-0.3464   Mean   : 0.07391   Mean   :-0.6731   Mean   :-0.1181  
##  3rd Qu.: 0.0000   3rd Qu.: 0.00000   3rd Qu.: 0.0000   3rd Qu.: 0.0000  
##  Max.   : 2.7494   Max.   : 3.16872   Max.   : 0.5314   Max.   : 3.1263  
##  Gemmiger_formicilis Guopingia_tenuis  Holdemania_filiformis
##  Min.   :-5.551      Min.   :-5.8281   Min.   :-5.709       
##  1st Qu.: 1.689      1st Qu.:-2.2014   1st Qu.:-1.619       
##  Median : 2.593      Median : 0.0000   Median : 0.000       
##  Mean   : 2.344      Mean   :-1.1973   Mean   :-0.830       
##  3rd Qu.: 3.434      3rd Qu.: 0.0000   3rd Qu.: 0.000       
##  Max.   : 5.954      Max.   : 0.2643   Max.   : 1.297       
##  Hydrogenoanaerobacterium_saccharovorans Intestinimonas_butyriciproducens
##  Min.   :-5.8536                         Min.   :-4.8159                 
##  1st Qu.: 0.0000                         1st Qu.:-1.5908                 
##  Median : 0.1442                         Median :-0.1448                 
##  Mean   : 0.4071                         Mean   :-0.7856                 
##  3rd Qu.: 1.0568                         3rd Qu.: 0.0000                 
##  Max.   : 3.2497                         Max.   : 3.4351                 
##  Intestinimonas_gabonensis Intestinimonas_massiliensis
##  Min.   :-5.5297           Min.   :-5.3991            
##  1st Qu.:-1.8054           1st Qu.:-0.9673            
##  Median :-0.6880           Median : 0.0000            
##  Mean   :-1.0503           Mean   :-0.4469            
##  3rd Qu.: 0.0000           3rd Qu.: 0.0000            
##  Max.   : 0.8567           Max.   : 3.2466            
##  Lachnoclostridium_sp_An138 Lachnospira_eligens Lachnospira_pectinoschiza
##  Min.   :-6.1261            Min.   :-4.0601     Min.   :-6.0273          
##  1st Qu.: 0.0000            1st Qu.: 0.0000     1st Qu.: 0.3644          
##  Median : 0.0000            Median : 0.9611     Median : 1.8097          
##  Mean   :-0.6742            Mean   : 1.1226     Mean   : 1.6724          
##  3rd Qu.: 0.0000            3rd Qu.: 2.5593     3rd Qu.: 2.9930          
##  Max.   : 0.0000            Max.   : 5.1842     Max.   : 5.8982          
##  Lachnospiraceae_bacterium Lachnospiraceae_bacterium_AM48_27BH
##  Min.   :-4.78137          Min.   :-6.2761                    
##  1st Qu.:-0.95541          1st Qu.:-0.9196                    
##  Median : 0.00000          Median : 0.0000                    
##  Mean   : 0.04254          Mean   :-0.3611                    
##  3rd Qu.: 1.26166          3rd Qu.: 0.4298                    
##  Max.   : 3.82406          Max.   : 2.4490                    
##  Lachnospiraceae_bacterium_CLA_AA_H215 Lachnospiraceae_bacterium_CLA_AA_H244
##  Min.   :-6.3304                       Min.   :-3.862                       
##  1st Qu.:-1.3246                       1st Qu.: 0.000                       
##  Median : 0.0000                       Median : 1.061                       
##  Mean   :-0.7616                       Mean   : 1.040                       
##  3rd Qu.: 0.0000                       3rd Qu.: 1.867                       
##  Max.   : 1.8505                       Max.   : 4.322                       
##  Lachnotalea_sp_AF33_28 Lacrimispora_amygdalina Lawsonibacter_SGB15145
##  Min.   :-6.7757        Min.   :-5.8052         Min.   :-5.4121       
##  1st Qu.:-2.6374        1st Qu.:-0.2405         1st Qu.:-0.5174       
##  Median : 0.0000        Median : 0.5614         Median : 0.0000       
##  Mean   :-1.3435        Mean   : 0.4253         Mean   :-0.3279       
##  3rd Qu.: 0.0000        3rd Qu.: 1.4613         3rd Qu.: 0.1997       
##  Max.   : 0.0807        Max.   : 2.8836         Max.   : 2.6373       
##  Lawsonibacter_asaccharolyticus Lawsonibacter_hominis Ligaoa_zhengdingensis
##  Min.   :-4.7540                Min.   :-6.1852       Min.   :-6.6062      
##  1st Qu.:-0.5325                1st Qu.:-1.2074       1st Qu.:-1.4531      
##  Median : 0.2685                Median : 0.0000       Median : 0.0000      
##  Mean   : 0.4549                Mean   :-0.5602       Mean   :-0.9759      
##  3rd Qu.: 1.8395                3rd Qu.: 0.0000       3rd Qu.: 0.0000      
##  Max.   : 4.6691                Max.   : 3.0564       Max.   : 0.0000      
##  Mediterraneibacter_faecis Odoribacter_splanchnicus Oliverpabstia_intestinalis
##  Min.   :-5.2996           Min.   :-3.9411          Min.   :-5.2171           
##  1st Qu.:-1.0579           1st Qu.: 0.0000          1st Qu.:-0.7777           
##  Median : 0.0000           Median : 0.8127          Median : 0.0000           
##  Mean   :-0.4471           Mean   : 0.7651          Mean   :-0.2479           
##  3rd Qu.: 0.2132           3rd Qu.: 1.6757          3rd Qu.: 0.0000           
##  Max.   : 2.7140           Max.   : 3.0476          Max.   : 3.5413           
##  Oscillibacter_sp_ER4 Oscillibacter_sp_MSJ_31 Oscillibacter_sp_PC13
##  Min.   :-4.295       Min.   :-5.907          Min.   :-5.987       
##  1st Qu.: 0.000       1st Qu.: 0.000          1st Qu.:-2.312       
##  Median : 2.384       Median : 1.049          Median : 0.000       
##  Mean   : 2.086       Mean   : 1.219          Mean   :-1.180       
##  3rd Qu.: 3.484       3rd Qu.: 3.039          3rd Qu.: 0.000       
##  Max.   : 5.434       Max.   : 6.375          Max.   : 0.000       
##  Oscillibacter_valericigenes Oscillospiraceae_bacterium
##  Min.   :-4.473              Min.   :-4.7967           
##  1st Qu.: 0.320              1st Qu.:-0.1854           
##  Median : 1.493              Median : 0.0000           
##  Mean   : 1.362              Mean   : 0.3729           
##  3rd Qu.: 2.509              3rd Qu.: 1.1587           
##  Max.   : 5.262              Max.   : 5.2059           
##  Oscillospiraceae_bacterium_CLA_AA_H250
##  Min.   :-4.54411                      
##  1st Qu.:-0.06459                      
##  Median : 0.05668                      
##  Mean   : 0.45041                      
##  3rd Qu.: 1.30189                      
##  Max.   : 3.89644                      
##  Oscillospiraceae_bacterium_Marseille_Q3528 Parabacteroides_distasonis
##  Min.   :-6.02552                           Min.   :-2.5911           
##  1st Qu.:-1.05026                           1st Qu.: 0.6096           
##  Median :-0.08802                           Median : 1.6607           
##  Mean   :-0.49883                           Mean   : 1.5234           
##  3rd Qu.: 0.00000                           3rd Qu.: 2.5314           
##  Max.   : 2.23785                           Max.   : 4.2565           
##  Parabacteroides_merdae Paraprevotella_clara Parasutterella_excrementihominis
##  Min.   :-2.585         Min.   :-7.582       Min.   :-5.70562                
##  1st Qu.: 0.000         1st Qu.: 0.000       1st Qu.:-0.58426                
##  Median : 1.692         Median : 0.000       Median : 0.00000                
##  Mean   : 1.472         Mean   : 0.684       Mean   :-0.04083                
##  3rd Qu.: 2.578         3rd Qu.: 2.521       3rd Qu.: 0.79667                
##  Max.   : 4.516         Max.   : 4.977       Max.   : 3.91225                
##  Phascolarctobacterium_faecium Phocaeicola_dorei Phocaeicola_sartorii
##  Min.   :-4.1832               Min.   :-5.6214   Min.   :-5.5937     
##  1st Qu.: 0.0000               1st Qu.: 0.0000   1st Qu.:-1.7440     
##  Median : 0.0000               Median : 0.7572   Median : 0.0000     
##  Mean   : 0.6681               Mean   : 1.1729   Mean   :-0.8716     
##  3rd Qu.: 1.3949               3rd Qu.: 3.0747   3rd Qu.: 0.0000     
##  Max.   : 5.3883               Max.   : 6.1807   Max.   : 0.0000     
##  Phocaeicola_vulgatus Phocea_massiliensis Provencibacterium_massiliense
##  Min.   :-5.741       Min.   :-5.1282     Min.   :-6.898               
##  1st Qu.: 2.321       1st Qu.:-1.3210     1st Qu.:-1.647               
##  Median : 3.299       Median : 0.0000     Median : 0.000               
##  Mean   : 3.020       Mean   :-0.7528     Mean   :-0.873               
##  3rd Qu.: 4.483       3rd Qu.: 0.0000     3rd Qu.: 0.000               
##  Max.   : 6.213       Max.   : 1.1089     Max.   : 0.000               
##  Pseudoflavonifractor_capillosus Roseburia_faecis Roseburia_hominis
##  Min.   :-5.4129                 Min.   :-7.226   Min.   :-5.944   
##  1st Qu.:-1.4330                 1st Qu.: 0.000   1st Qu.: 0.000   
##  Median : 0.0000                 Median : 1.162   Median : 1.223   
##  Mean   :-0.6951                 Mean   : 1.199   Mean   : 1.133   
##  3rd Qu.: 0.0000                 3rd Qu.: 2.552   3rd Qu.: 2.280   
##  Max.   : 3.7610                 Max.   : 5.930   Max.   : 4.916   
##  Roseburia_intestinalis Roseburia_inulinivorans Ruminococcus_bicirculans
##  Min.   :-5.17217       Min.   :-5.8540         Min.   :-5.0535         
##  1st Qu.:-0.22793       1st Qu.:-0.1915         1st Qu.: 0.0000         
##  Median : 0.00000       Median : 0.9222         Median : 0.4475         
##  Mean   : 0.08328       Mean   : 0.7964         Mean   : 0.7507         
##  3rd Qu.: 1.09541       3rd Qu.: 2.0758         3rd Qu.: 1.9562         
##  Max.   : 4.72592       Max.   : 4.7512         Max.   : 4.6842         
##  Ruminococcus_bromii Ruminococcus_torques Ruthenibacterium_lactatiformans
##  Min.   :-5.769      Min.   :-6.2174      Min.   :-2.9670                
##  1st Qu.: 0.000      1st Qu.:-0.7056      1st Qu.:-0.4346                
##  Median : 1.089      Median : 0.0000      Median : 0.2900                
##  Mean   : 1.252      Mean   :-0.4239      Mean   : 0.3920                
##  3rd Qu.: 2.710      3rd Qu.: 0.0000      3rd Qu.: 1.1876                
##  Max.   : 5.144      Max.   : 2.6706      Max.   : 4.8960                
##  Segatella_copri  Simiaoa_sunii     Streptococcus_salivarius
##  Min.   :-6.121   Min.   :-4.7315   Min.   :-5.6677         
##  1st Qu.: 0.000   1st Qu.:-1.0608   1st Qu.:-1.8696         
##  Median : 0.000   Median : 0.0000   Median :-0.2559         
##  Mean   : 1.093   Mean   : 0.2712   Mean   :-0.9178         
##  3rd Qu.: 2.186   3rd Qu.: 1.6911   3rd Qu.: 0.0000         
##  Max.   : 8.859   Max.   : 5.7028   Max.   : 2.6156         
##  Streptococcus_thermophilus Sutterella_wadsworthensis Vescimonas_coprocola
##  Min.   :-4.2691            Min.   :-6.6268           Min.   :-3.6998     
##  1st Qu.:-0.2553            1st Qu.: 0.0000           1st Qu.:-0.3805     
##  Median : 0.0000            Median : 0.1828           Median : 0.0000     
##  Mean   :-0.3109            Mean   : 1.2046           Mean   : 0.3509     
##  3rd Qu.: 0.0000            3rd Qu.: 3.1077           3rd Qu.: 1.5151     
##  Max.   : 3.1085            Max.   : 5.7922           Max.   : 4.3114     
##  Wansuia_hejianensis Youxingia_wuxianensis bacterium_210917_DFI_7_65
##  Min.   :-7.195      Min.   :-7.385        Min.   :-6.1955          
##  1st Qu.:-3.003      1st Qu.:-2.699        1st Qu.:-1.0582          
##  Median : 0.000      Median : 0.000        Median : 0.0000          
##  Mean   :-1.400      Mean   :-1.337        Mean   :-0.5379          
##  3rd Qu.: 0.000      3rd Qu.: 0.000        3rd Qu.: 0.0000          
##  Max.   : 0.000      Max.   : 0.000        Max.   : 1.7357          
##  Bacteroides_faecis Clostridiaceae_unclassified_SGB4771 Clostridium_sp_AM49_4BH
##  Min.   :-6.9192    Min.   :-6.6655                     Min.   :-5.5937        
##  1st Qu.: 0.0000    1st Qu.:-0.4258                     1st Qu.: 0.0000        
##  Median : 0.0000    Median : 0.0000                     Median : 0.0000        
##  Mean   : 0.4013    Mean   :-0.3298                     Mean   : 0.1470        
##  3rd Qu.: 0.4889    3rd Qu.: 0.0000                     3rd Qu.: 0.6252        
##  Max.   : 5.0083    Max.   : 3.1516                     Max.   : 3.6837        
##  Colidextribacter_sp_210702_DFI_3_9 Enterocloster_lavalensis GGB2982_SGB3964  
##  Min.   :-4.6854                    Min.   :-6.4898          Min.   :-5.4601  
##  1st Qu.:-0.7781                    1st Qu.:-1.6643          1st Qu.:-0.8472  
##  Median : 0.0000                    Median : 0.0000          Median : 0.0000  
##  Mean   :-0.5236                    Mean   :-0.9849          Mean   :-0.4751  
##  3rd Qu.: 0.0000                    3rd Qu.: 0.0000          3rd Qu.: 0.0000  
##  Max.   : 1.9906                    Max.   : 0.3161          Max.   : 1.8903  
##  GGB3304_SGB4367   GGB3619_SGB4894   GGB9296_SGB14253  GGB9524_SGB14924 
##  Min.   :-5.9559   Min.   :-3.8900   Min.   :-4.9269   Min.   :-4.2068  
##  1st Qu.: 0.0000   1st Qu.: 0.0000   1st Qu.: 0.0000   1st Qu.:-0.0594  
##  Median : 0.0000   Median : 0.0000   Median : 0.0000   Median : 0.0000  
##  Mean   : 0.8212   Mean   :-0.1701   Mean   :-0.1924   Mean   :-0.2527  
##  3rd Qu.: 2.4033   3rd Qu.: 0.0000   3rd Qu.: 0.0000   3rd Qu.: 0.0000  
##  Max.   : 5.5587   Max.   : 3.7075   Max.   : 2.6320   Max.   : 3.9873  
##  GGB9574_SGB14987  GGB9619_SGB15066  GGB9707_SGB15229  GGB9708_SGB15233  
##  Min.   :-6.0739   Min.   :-6.6626   Min.   :-3.1017   Min.   :-6.45619  
##  1st Qu.:-1.1269   1st Qu.: 0.0000   1st Qu.: 0.0000   1st Qu.: 0.00000  
##  Median : 0.0000   Median : 0.0000   Median : 0.0000   Median : 0.00000  
##  Mean   :-0.7441   Mean   :-0.3097   Mean   : 0.5169   Mean   :-0.03637  
##  3rd Qu.: 0.0000   3rd Qu.: 0.0000   3rd Qu.: 1.2956   3rd Qu.: 0.02548  
##  Max.   : 0.6636   Max.   : 1.8983   Max.   : 4.1015   Max.   : 5.58215  
##  GGB9760_SGB15374  Roseburia_sp_AF02_12 Segatella_brunsvicensis
##  Min.   :-5.7911   Min.   :-5.0396      Min.   :-6.4159        
##  1st Qu.: 0.0000   1st Qu.:-1.0317      1st Qu.: 0.0000        
##  Median : 0.0000   Median : 0.0000      Median : 0.0000        
##  Mean   : 0.1243   Mean   :-0.3165      Mean   : 0.1079        
##  3rd Qu.: 0.3593   3rd Qu.: 0.0000      3rd Qu.: 0.0000        
##  Max.   : 3.5431   Max.   : 4.0833      Max.   : 8.5476        
##  Wujia_chipingensis Alistipes_dispar  Alistipes_sp_AF17_16
##  Min.   :-6.7006    Min.   :-4.8419   Min.   :-4.0321     
##  1st Qu.: 0.0000    1st Qu.: 0.0000   1st Qu.: 0.0000     
##  Median : 0.0000    Median : 0.0000   Median : 0.0000     
##  Mean   : 0.4702    Mean   : 0.1859   Mean   : 0.2998     
##  3rd Qu.: 1.5460    3rd Qu.: 0.0000   3rd Qu.: 0.5336     
##  Max.   : 5.0594    Max.   : 4.0537   Max.   : 4.4258     
##  Anaerobutyricum_soehngenii Anaerosacchariphilus_sp_NSJ_68
##  Min.   :-5.3029            Min.   :-6.6105               
##  1st Qu.:-0.8211            1st Qu.:-2.1414               
##  Median : 0.0000            Median : 0.0000               
##  Mean   :-0.6380            Mean   :-1.1408               
##  3rd Qu.: 0.0000            3rd Qu.: 0.0000               
##  Max.   : 2.7147            Max.   : 0.3643               
##  Anaerotignum_sp_MSJ_24 Bittarella_massiliensis Blautia_SGB4815  
##  Min.   :-4.3845        Min.   :-5.2521         Min.   :-5.8095  
##  1st Qu.:-1.0088        1st Qu.: 0.0000         1st Qu.:-1.8332  
##  Median : 0.0000        Median : 0.0000         Median :-0.1304  
##  Mean   :-0.5936        Mean   :-0.6922         Mean   :-1.0063  
##  3rd Qu.: 0.0000        3rd Qu.: 0.0000         3rd Qu.: 0.0000  
##  Max.   : 0.4821        Max.   : 0.0000         Max.   : 1.5363  
##   Blautia_luti     Blautia_sp_OF03_15BH Butyricimonas_paravirosa
##  Min.   :-5.9243   Min.   :-5.48886     Min.   :-6.0500         
##  1st Qu.:-0.8782   1st Qu.:-1.16625     1st Qu.: 0.0000         
##  Median : 0.0000   Median : 0.00000     Median : 0.0000         
##  Mean   :-0.6830   Mean   :-0.75686     Mean   :-0.3684         
##  3rd Qu.: 0.0000   3rd Qu.: 0.00000     3rd Qu.: 0.0000         
##  Max.   : 2.9218   Max.   : 0.08327     Max.   : 1.8108         
##  Catenibacillus_scindens Clostridiaceae_bacterium_Marseille_Q4149
##  Min.   :-7.0889         Min.   :-5.0521                         
##  1st Qu.: 0.0000         1st Qu.: 0.0000                         
##  Median : 0.0000         Median : 0.0000                         
##  Mean   :-0.5142         Mean   : 0.3234                         
##  3rd Qu.: 0.0000         3rd Qu.: 0.1292                         
##  Max.   : 0.0000         Max.   : 5.7042                         
##  Clostridium_SGB6173 Clostridium_SGB6179 Clostridium_sp_Marseille_P3244
##  Min.   :-6.083      Min.   :-5.078      Min.   :-6.9192               
##  1st Qu.: 0.000      1st Qu.: 0.000      1st Qu.: 0.0000               
##  Median : 0.000      Median : 0.000      Median : 0.0000               
##  Mean   :-0.327      Mean   :-0.309      Mean   :-0.6426               
##  3rd Qu.: 0.000      3rd Qu.: 0.000      3rd Qu.: 0.0000               
##  Max.   : 3.230      Max.   : 3.402      Max.   : 0.0000               
##  Clostridium_sp_NSJ_42 Coprobacter_secundus Eubacteriaceae_bacterium
##  Min.   :-5.7599       Min.   :-6.2571      Min.   :-5.8953         
##  1st Qu.: 0.0000       1st Qu.:-0.6748      1st Qu.:-1.5891         
##  Median : 0.0000       Median : 0.0000      Median : 0.0000         
##  Mean   :-0.2637       Mean   :-0.6056      Mean   :-0.6869         
##  3rd Qu.: 0.0000       3rd Qu.: 0.0000      3rd Qu.: 0.0000         
##  Max.   : 3.4751       Max.   : 1.4822      Max.   : 5.2795         
##  Faecalibacillus_faecis Faecalibacillus_intestinalis GGB13489_SGB15224
##  Min.   :-5.0189        Min.   :-5.9421              Min.   :-3.3026  
##  1st Qu.: 0.0000        1st Qu.:-0.1373              1st Qu.: 0.0000  
##  Median : 0.0000        Median : 0.0000              Median : 0.0000  
##  Mean   :-0.4155        Mean   :-0.1286              Mean   : 0.2069  
##  3rd Qu.: 0.0000        3rd Qu.: 0.7427              3rd Qu.: 0.2068  
##  Max.   : 2.6455        Max.   : 3.0314              Max.   : 3.0282  
##  GGB2970_SGB3952   GGB3352_SGB4436    GGB34797_SGB14322 GGB34900_SGB14891
##  Min.   :-2.8095   Min.   :-5.96473   Min.   :-3.241    Min.   :-6.2276  
##  1st Qu.: 0.0000   1st Qu.: 0.00000   1st Qu.: 0.000    1st Qu.: 0.0000  
##  Median : 0.0000   Median : 0.00000   Median : 0.000    Median : 0.0000  
##  Mean   :-0.2337   Mean   :-0.48520   Mean   :-0.141    Mean   :-0.6567  
##  3rd Qu.: 0.0000   3rd Qu.: 0.00000   3rd Qu.: 0.000    3rd Qu.: 0.0000  
##  Max.   : 1.3542   Max.   : 0.09886   Max.   : 2.295    Max.   : 0.0000  
##  GGB3653_SGB4964     GGB4456_SGB6141   GGB4552_SGB6276   GGB51441_SGB71759
##  Min.   :-5.452216   Min.   :-6.2652   Min.   :-7.1084   Min.   :-5.945   
##  1st Qu.: 0.000000   1st Qu.: 0.0000   1st Qu.: 0.0000   1st Qu.:-1.928   
##  Median : 0.000000   Median : 0.0000   Median : 0.0000   Median :-0.549   
##  Mean   :-0.084483   Mean   :-0.4249   Mean   : 0.3139   Mean   :-1.008   
##  3rd Qu.: 0.007261   3rd Qu.: 0.0000   3rd Qu.: 0.6365   3rd Qu.: 0.000   
##  Max.   : 2.658404   Max.   : 0.9505   Max.   : 4.5068   Max.   : 2.068   
##  GGB58158_SGB79798 GGB9365_SGB14341  GGB9412_SGB14770  GGB9627_SGB15081 
##  Min.   :-7.326    Min.   :-3.9307   Min.   :-4.9282   Min.   :-4.0878  
##  1st Qu.:-2.388    1st Qu.:-0.4118   1st Qu.: 0.0000   1st Qu.: 0.0000  
##  Median : 0.000    Median : 0.0000   Median : 0.0000   Median : 0.0000  
##  Mean   :-1.124    Mean   :-0.4366   Mean   :-0.1863   Mean   : 0.3138  
##  3rd Qu.: 0.000    3rd Qu.: 0.0000   3rd Qu.: 0.0000   3rd Qu.: 0.6756  
##  Max.   : 0.000    Max.   : 2.8745   Max.   : 2.7674   Max.   : 3.2518  
##  GGB9712_SGB15244  GGB9747_SGB15356  GGB9767_SGB15385  GGB9787_SGB15410 
##  Min.   :-5.0027   Min.   :-5.8601   Min.   :-4.9249   Min.   :-6.2847  
##  1st Qu.: 0.0000   1st Qu.: 0.0000   1st Qu.: 0.0000   1st Qu.: 0.0000  
##  Median : 0.0000   Median : 0.0000   Median : 0.0000   Median : 0.0000  
##  Mean   : 0.3142   Mean   : 0.6813   Mean   :-0.1288   Mean   :-0.4331  
##  3rd Qu.: 0.0000   3rd Qu.: 1.7292   3rd Qu.: 0.0000   3rd Qu.: 0.0000  
##  Max.   : 4.5076   Max.   : 5.1183   Max.   : 2.6607   Max.   : 1.3411  
##  GGB9790_SGB15413  Haemophilus_parainfluenzae Intestinibacter_bartlettii
##  Min.   :-5.2667   Min.   :-4.4106            Min.   :-5.0906           
##  1st Qu.: 0.0000   1st Qu.:-1.7155            1st Qu.:-0.5591           
##  Median : 0.0000   Median : 0.0000            Median : 0.0000           
##  Mean   :-0.2979   Mean   :-0.8484            Mean   :-0.4847           
##  3rd Qu.: 0.0000   3rd Qu.: 0.0000            3rd Qu.: 0.0000           
##  Max.   : 1.5817   Max.   : 1.2033            Max.   : 1.8226           
##  Lachnospira_sp_NSJ_43 Lachnospiraceae_bacterium_OM04_12BH Lactococcus_lactis
##  Min.   :-4.2193       Min.   :-5.8053                     Min.   :-4.1685   
##  1st Qu.: 0.0000       1st Qu.:-0.7840                     1st Qu.: 0.0000   
##  Median : 0.0000       Median : 0.0000                     Median : 0.0000   
##  Mean   : 0.3480       Mean   :-0.6651                     Mean   :-0.1791   
##  3rd Qu.: 0.9412       3rd Qu.: 0.0000                     3rd Qu.: 0.0000   
##  Max.   : 4.6982       Max.   : 2.6057                     Max.   : 2.2243   
##  Lentihominibacter_faecis Massilioclostridium_coli
##  Min.   :-6.0609          Min.   :-7.2232         
##  1st Qu.:-1.6673          1st Qu.:-0.9072         
##  Median : 0.0000          Median : 0.0000         
##  Mean   :-0.9779          Mean   :-0.7921         
##  3rd Qu.: 0.0000          3rd Qu.: 0.0000         
##  Max.   : 2.0767          Max.   : 0.8236         
##  Mediterraneibacter_butyricigenes Mediterraneibacter_sp_NSJ_151
##  Min.   :-6.744                   Min.   :-4.2915              
##  1st Qu.:-2.882                   1st Qu.: 0.0000              
##  Median :-1.285                   Median : 0.0000              
##  Mean   :-1.584                   Mean   :-0.3781              
##  3rd Qu.: 0.000                   3rd Qu.: 0.0000              
##  Max.   : 0.000                   Max.   : 0.0000              
##  Methanobrevibacter_smithii Romboutsia_timonensis Ruminococcus_gnavus
##  Min.   :-5.15172           Min.   :-5.6214       Min.   :-6.2707    
##  1st Qu.: 0.00000           1st Qu.:-0.5506       1st Qu.:-1.6294    
##  Median : 0.00000           Median : 0.0000       Median : 0.0000    
##  Mean   : 0.09254           Mean   :-0.3860       Mean   :-0.8162    
##  3rd Qu.: 0.00000           3rd Qu.: 0.0000       3rd Qu.: 0.0000    
##  Max.   : 6.45727           Max.   : 3.1234       Max.   : 4.5988    
##  Ruminococcus_lactaris Ruminococcus_sp_AF41_9 Senegalimassilia_anaerobia
##  Min.   :-5.75627      Min.   :-5.3581        Min.   :-4.6477           
##  1st Qu.: 0.00000      1st Qu.: 0.0000        1st Qu.:-0.5257           
##  Median : 0.00000      Median : 0.0000        Median : 0.0000           
##  Mean   :-0.01148      Mean   :-0.2957        Mean   :-0.3788           
##  3rd Qu.: 0.38389      3rd Qu.: 0.0000        3rd Qu.: 0.0000           
##  Max.   : 3.36317      Max.   : 2.5332        Max.   : 1.5076           
##  Slackia_isoflavoniconvertens Streptococcus_parasanguinis Veillonella_dispar
##  Min.   :-2.91078             Min.   :-6.2756             Min.   :-6.2739   
##  1st Qu.: 0.00000             1st Qu.:-2.1707             1st Qu.:-1.1894   
##  Median : 0.00000             Median : 0.0000             Median : 0.0000   
##  Mean   : 0.03323             Mean   :-1.1185             Mean   :-0.7324   
##  3rd Qu.: 0.00000             3rd Qu.: 0.0000             3rd Qu.: 0.0000   
##  Max.   : 2.60620             Max.   : 0.9195             Max.   : 1.5623   
##  Victivallis_lenta Bifidobacterium_pseudocatenulatum Eubacterium_sp_AF34_35BH
##  Min.   :-5.6533   Min.   :-4.831605                 Min.   :-5.2777         
##  1st Qu.: 0.0000   1st Qu.: 0.000000                 1st Qu.:-0.1684         
##  Median : 0.0000   Median : 0.000000                 Median : 0.0000         
##  Mean   : 0.1367   Mean   :-0.000609                 Mean   :-0.3399         
##  3rd Qu.: 0.0000   3rd Qu.: 0.000000                 3rd Qu.: 0.0000         
##  Max.   : 3.5130   Max.   : 3.718131                 Max.   : 1.3687         
##  Faecalicatena_contorta GGB9559_SGB14969  GGB9759_SGB15370  Roseburia_lenta   
##  Min.   :-6.9017        Min.   :-5.6428   Min.   :-4.7775   Min.   :-3.11486  
##  1st Qu.: 0.0000        1st Qu.:-1.0706   1st Qu.: 0.0000   1st Qu.: 0.00000  
##  Median : 0.0000        Median : 0.0000   Median : 0.0000   Median : 0.00000  
##  Mean   :-0.6991        Mean   :-0.7472   Mean   :-0.1596   Mean   : 0.28856  
##  3rd Qu.: 0.0000        3rd Qu.: 0.0000   3rd Qu.: 0.0000   3rd Qu.: 0.02958  
##  Max.   : 0.0000        Max.   : 0.8908   Max.   : 2.1550   Max.   : 4.02433  
##  Enterocloster_bolteae GGB2848_SGB3813  GGB3005_SGB3996   GGB3061_SGB4063  
##  Min.   :-5.530        Min.   :-6.469   Min.   :-6.4363   Min.   :-5.2983  
##  1st Qu.:-1.858        1st Qu.:-2.216   1st Qu.:-1.1200   1st Qu.: 0.0000  
##  Median : 0.000        Median : 0.000   Median : 0.0000   Median : 0.0000  
##  Mean   :-1.046        Mean   :-1.072   Mean   :-0.7651   Mean   :-0.3932  
##  3rd Qu.: 0.000        3rd Qu.: 0.000   3rd Qu.: 0.0000   3rd Qu.: 0.0000  
##  Max.   : 1.563        Max.   : 1.288   Max.   : 1.0962   Max.   : 0.9089  
##  GGB36331_SGB15121 Hungatella_hathewayi TM7_phylum_sp_oral_taxon_352
##  Min.   :-5.6253   Min.   :-6.4091      Min.   :-4.6915             
##  1st Qu.: 0.0000   1st Qu.:-1.4589      1st Qu.:-2.3671             
##  Median : 0.0000   Median : 0.0000      Median : 0.0000             
##  Mean   :-0.1716   Mean   :-0.8347      Mean   :-1.2015             
##  3rd Qu.: 0.0000   3rd Qu.: 0.0000      3rd Qu.: 0.0000             
##  Max.   : 1.8458   Max.   : 4.7239      Max.   : 0.9325             
##  Veillonella_parvula GGB6649_SGB9391     Veillonella_atypica
##  Min.   :-5.8684     Min.   :-4.504849   Min.   :-5.6143    
##  1st Qu.:-1.6149     1st Qu.: 0.000000   1st Qu.:-1.1989    
##  Median : 0.0000     Median : 0.000000   Median : 0.0000    
##  Mean   :-0.8513     Mean   : 0.006198   Mean   :-0.6422    
##  3rd Qu.: 0.0000     3rd Qu.: 0.062313   3rd Qu.: 0.0000    
##  Max.   : 2.3069     Max.   : 2.259711   Max.   : 1.6658

3.2.1.1 Distributions - clr transformed

Open code
check <- data_microbiome_original %>% 
  dplyr::select(
    Adlercreutzia_equolifaciens:Veillonella_atypica
    ) %>% 
  na.omit()


size = c(8, 7)
par(mfrow = c(size[1],size[2]))
par(mar=c(2,1.5,2,0.5))
set.seed(16)
ran <- sample(1:ncol(check), size[1]*size[2], replace = FALSE)
for(x in ran){
  hist(check[,x], 
       16, 
       col='blue', 
       main = paste0(colnames(check)[x])
  )
}

Histogram of CLR-transformed proportions for a random selection of 56 bacterial taxa (proportion: number of sequences for each bacterium relative to the total library depth)

3.2.1.2 Comparison training vs validation cohort

Open code
check <- data_merged %>% select(-Data, -Diet)

size = c(8,7)
ran <- sample(1:ncol(check), size[1]*size[2], replace = FALSE)

par(mfrow = c(size[1],size[2]))
par(mar = c(2,1.5,2,0.5))
par(mgp = c(3, 0.5, 0 ))

for(x in ran){
  plot(
    data_merged[, x+2] ~ factor(data_merged$Data),
       main = paste0(colnames(check)[x])
  )
}

Boxplot showing clr-transformed counta across both training cohorts but also in independent validation cohort

3.2.1.3 Metabolites accross groups

Open code
colo <- c('#329243', '#F9FFAF')

data_merged <- na.omit(data_merged)

outcomes <- common_microbiome[
    sample(
      1:length(common_microbiome), 35, replace = FALSE
      )
  ]

boxplot_cond <- function(variable) {
  
  
  p <- ggboxplot(data_merged, 
                 x = 'Diet', 
                 y = variable, 
                 fill = 'Diet', 
                 tip.length = 0.15,
                 palette = colo,
                 outlier.shape = 1,
                 lwd = 0.25,
                 outlier.size = 0.8,
                 facet.by = 'Data',
                 title = variable,
                 ylab = 'Lipid level') +
    
    theme(
      plot.title = element_text(size = 10), 
      axis.title = element_text(size = 8),  
      axis.text.y = element_text(size = 7),
      axis.text.x = element_blank(),
      axis.title.x = element_blank()
    ) 
    
  
  return(p)
}

# Plot all outcomes
plots <- map(outcomes, boxplot_cond)

# Create a matrix of plots
plots_arranged <- ggarrange(plotlist = plots, ncol = 5, nrow = 7,  common.legend = TRUE)
plots_arranged

CLR-trasformed bacteria counts across all 3 cohorts (Czech and Italian training cohorts and an independent Czech valdiation cohort) and across dietary groups

4 Linear models across taxa

We will fit a feature-specific linear model where the CLR-transformed count of bacteria reads represents the outcome variable whereas country (Italy vs Czech), diet (vegan vs omnivore), and their interaction (country:diet) all represent fixed-effects predictors. So, each model has the following form

\[ CLR({N_i}) = \alpha + \beta_{1} \times country + \beta_{2} \times diet + \beta_{3} \times country:diet + \epsilon \] where \(N_i\) is read count of \(i\)-th bacteria taxa

The variables were coded as follows: \(diet = -0.5\) for omnivores and \(diet = 0.5\) for vegans; \(country = -0.5\) for the Czech cohort and \(country = 0.5\) for the Italian cohort.
This parameterization allows us to interpret the linear model summary output as presenting the conditional effects of diet averaged across both countries and the conditional effects of country averaged across both diet groups. We will then use the emmeans package (Lenth 2024) to obtain specific estimates for the effect of diet in the Italian and Czech cohorts separately, still from a single model.

Taxa that will show a significant diet effect (average effect of diet across both countries, adjusted for multiple comparisons with FDR < 0.1) will be then visualized using a forest plot, with country-specific diet effect along with diet effect based on independent validation cohort, to evaluate how generalizable these findings are (see external validation section).

Note that p-value for avg effects are the same as produced with car::Anova(model, type = 'III').

4.1 Select data

Open code
data_analysis <- data_microbiome_original %>%
  na.omit() %>%
  dplyr::mutate(
    Diet_VEGAN = as.numeric(
      dplyr::if_else(
        Diet == "VEGAN", 0.5, -0.5
      )
    ),
    Country_IT = as.numeric(
      dplyr::if_else(
        Country == "IT", 0.5, -0.5
      )
    )
  ) %>%
  dplyr::select(
    Sample,
    Country,
    Country_IT,
    Diet,
    Diet_VEGAN,
    dplyr::everything()
  )

summary(data_analysis[ , 1:12])
##     Sample            Country            Country_IT           Diet          
##  Length:166         Length:166         Min.   :-0.50000   Length:166        
##  Class :character   Class :character   1st Qu.:-0.50000   Class :character  
##  Mode  :character   Mode  :character   Median :-0.50000   Mode  :character  
##                                        Mean   :-0.03012                     
##                                        3rd Qu.: 0.50000                     
##                                        Max.   : 0.50000                     
##    Diet_VEGAN       Adlercreutzia_equolifaciens Agathobaculum_butyriciproducens
##  Min.   :-0.50000   Min.   :-5.3879             Min.   :-1.6741                
##  1st Qu.:-0.50000   1st Qu.:-1.8236             1st Qu.: 0.9966                
##  Median : 0.50000   Median :-0.3954             Median : 1.7080                
##  Mean   : 0.08434   Mean   :-0.9361             Mean   : 1.6332                
##  3rd Qu.: 0.50000   3rd Qu.: 0.0000             3rd Qu.: 2.3623                
##  Max.   : 0.50000   Max.   : 2.9097             Max.   : 4.1360                
##  Akkermansia_muciniphila Alistipes_communis Alistipes_finegoldii
##  Min.   :-5.961          Min.   :-4.579     Min.   :-5.9534     
##  1st Qu.: 0.000          1st Qu.: 0.000     1st Qu.: 0.0000     
##  Median : 1.018          Median : 1.911     Median : 0.4529     
##  Mean   : 1.437          Mean   : 1.666     Mean   : 0.8876     
##  3rd Qu.: 3.155          3rd Qu.: 2.925     3rd Qu.: 2.0030     
##  Max.   : 7.112          Max.   : 5.808     Max.   : 5.2364     
##  Alistipes_ihumii  Alistipes_indistinctus
##  Min.   :-4.4586   Min.   :-5.34668      
##  1st Qu.: 0.0000   1st Qu.:-0.46130      
##  Median : 0.1777   Median : 0.00000      
##  Mean   : 0.8382   Mean   :-0.05192      
##  3rd Qu.: 1.8759   3rd Qu.: 0.60784      
##  Max.   : 4.4281   Max.   : 3.54569

4.1.1 Define number of microbiome and covariates

Open code
n_covarites <- 5
n_features <- ncol(data_analysis) - n_covarites

4.1.2 Create empty objects

Open code
outcome <- vector('double', n_features)
logFD_VGdiet_inCZ <- vector('double', n_features)
logFD_VGdiet_inIT <- vector('double', n_features)
logFD_VGdiet_avg <- vector('double', n_features)

logFD_ITcountry_avg <- vector('double', n_features)
diet_country_int <- vector('double', n_features)


P_VGdiet_inCZ <- vector('double', n_features)
P_VGdiet_inIT <- vector('double', n_features)
P_VGdiet_avg <- vector('double', n_features)

P_ITcountry_avg <- vector('double', n_features)
P_diet_country_int <- vector('double', n_features)


CI_L_VGdiet_inCZ <- vector('double', n_features)
CI_L_VGdiet_inIT <- vector('double', n_features)
CI_L_VGdiet_avg <- vector('double', n_features)

CI_U_VGdiet_inCZ <- vector('double', n_features)
CI_U_VGdiet_inIT <- vector('double', n_features)
CI_U_VGdiet_avg <- vector('double', n_features)

4.1.3 Estimate over outcomes

Open code
for (i in 1:n_features) {
  
  ## define variable
  data_analysis$outcome <- data_analysis[, (i + n_covarites)]

  ## fit model
  model <- lm(outcome ~ Country_IT * Diet_VEGAN, data = data_analysis)

  ## get contrast (effects of diet BY COUNTRY)
  contrast_emm <- summary(
    pairs(
      emmeans(
        model,
        specs = ~ Diet_VEGAN | Country_IT
        ),
      interaction = TRUE,
      adjust = "none"
      ),
    infer = c(TRUE, TRUE)
    )

  ## save results
  outcome[i] <- names(data_analysis)[i + n_covarites]
  
  ## country effect
  logFD_ITcountry_avg[i] <- summary(model)$coefficients[
    which(
      names(model$coefficients) == "Country_IT"
    ), 1
  ]

  P_ITcountry_avg[i] <- summary(model)$coefficients[
    which(
      names(model$coefficients) == "Country_IT"
    ), 4
  ]
  
  
  ## diet effect
  tr <- confint(model)
  
  CI_L_VGdiet_avg[i] <- tr[which(row.names(tr) == 'Diet_VEGAN'),][1]
  CI_U_VGdiet_avg[i] <- tr[which(row.names(tr) == 'Diet_VEGAN'),][2]
  
  logFD_VGdiet_avg[i] <- summary(model)$coefficients[
    which(
      names(model$coefficients) == "Diet_VEGAN"
    ), 1
  ]

  P_VGdiet_avg[i] <- summary(model)$coefficients[
    which(
      names(model$coefficients) == "Diet_VEGAN"
    ), 4
  ]
  
  logFD_VGdiet_inCZ[i] <- -contrast_emm[1,3]
  P_VGdiet_inCZ[i] <- contrast_emm$p.value[1]
  CI_L_VGdiet_inCZ[i] <- -contrast_emm$upper.CL[1]
  CI_U_VGdiet_inCZ[i] <- -contrast_emm$lower.CL[1]
  
  logFD_VGdiet_inIT[i] <- -contrast_emm[2,3]
  P_VGdiet_inIT[i] <- contrast_emm$p.value[2]
  CI_L_VGdiet_inIT[i] <- -contrast_emm$upper.CL[2]
  CI_U_VGdiet_inIT[i] <- -contrast_emm$lower.CL[2]
  
  ## interaction
  diet_country_int[i] <- summary(model)$coefficients[
    which(
      names(model$coefficients) == "Country_IT:Diet_VEGAN"
    ), 1
  ]

  P_diet_country_int[i] <- summary(model)$coefficients[
    which(
      names(model$coefficients) == "Country_IT:Diet_VEGAN"
    ), 4
  ]
}

4.1.4 Results table

Open code
result_microbiome <- data.frame(
  outcome,
  logFD_ITcountry_avg, P_ITcountry_avg,
  logFD_VGdiet_avg, P_VGdiet_avg,
  logFD_VGdiet_inCZ, P_VGdiet_inCZ,
  logFD_VGdiet_inIT, P_VGdiet_inIT,
  diet_country_int, P_diet_country_int,
  CI_L_VGdiet_avg, CI_U_VGdiet_avg,
  CI_L_VGdiet_inCZ, CI_U_VGdiet_inCZ,
  CI_L_VGdiet_inIT, CI_U_VGdiet_inIT
)

4.1.5 Adjust p values

Open code
result_microbiome <- result_microbiome %>% 
  dplyr::mutate(
    fdr_ITcountry_avg = p.adjust(P_ITcountry_avg, method = 'BH'),
    fdr_VGdiet_avg = p.adjust(P_VGdiet_avg, method = 'BH'),
    
    fdr_VGdiet_inCZ = p.adjust(P_VGdiet_inCZ, method = 'BH'),
    fdr_VGdiet_inIT = p.adjust(P_VGdiet_inIT, method = 'BH'),
    fdr_diet_country_int = p.adjust(P_diet_country_int, method = 'BH')
  ) %>% 
  dplyr::select(
    outcome,
    logFD_ITcountry_avg, P_ITcountry_avg, fdr_ITcountry_avg,
    logFD_VGdiet_avg, P_VGdiet_avg, fdr_VGdiet_avg,
    logFD_VGdiet_inCZ, P_VGdiet_inCZ, fdr_VGdiet_inCZ,
    logFD_VGdiet_inIT, P_VGdiet_inIT, fdr_VGdiet_inIT,
    diet_country_int, P_diet_country_int, fdr_diet_country_int,
    CI_L_VGdiet_avg, CI_U_VGdiet_avg,
    CI_L_VGdiet_inCZ, CI_U_VGdiet_inCZ,
    CI_L_VGdiet_inIT, CI_U_VGdiet_inIT
  )

4.1.6 Show and save results

Open code
kableExtra::kable(result_microbiome,
  caption = "Result of linear models, modelling the CLR-transformed reads count of given bacterial taxa, with `Diet`, `Country` and `Diet:Country` interaction as predictors. `logFD` prefix: implies estimated effects (regression coefficient), i.e. how much CLR-transformed reads count differ in vegans compared to omnivores, `P`: p-value, `fdr`: p-value after adjustment for multiple comparison, `CI_L` and `CI_U`: lower and upper bounds of 95% confidence interval respectively. `avg` suffix shows effect averaged across subgroups, whereas `inCZ` and `inIT` shows effect in Czech or Italian cohort respectively. All estimates in a single row are based on a single model"
)
Result of linear models, modelling the CLR-transformed reads count of given bacterial taxa, with Diet, Country and Diet:Country interaction as predictors. logFD prefix: implies estimated effects (regression coefficient), i.e. how much CLR-transformed reads count differ in vegans compared to omnivores, P: p-value, fdr: p-value after adjustment for multiple comparison, CI_L and CI_U: lower and upper bounds of 95% confidence interval respectively. avg suffix shows effect averaged across subgroups, whereas inCZ and inIT shows effect in Czech or Italian cohort respectively. All estimates in a single row are based on a single model
outcome logFD_ITcountry_avg P_ITcountry_avg fdr_ITcountry_avg logFD_VGdiet_avg P_VGdiet_avg fdr_VGdiet_avg logFD_VGdiet_inCZ P_VGdiet_inCZ fdr_VGdiet_inCZ logFD_VGdiet_inIT P_VGdiet_inIT fdr_VGdiet_inIT diet_country_int P_diet_country_int fdr_diet_country_int CI_L_VGdiet_avg CI_U_VGdiet_avg CI_L_VGdiet_inCZ CI_U_VGdiet_inCZ CI_L_VGdiet_inIT CI_U_VGdiet_inIT
Adlercreutzia_equolifaciens -0.0614960 0.7942844 0.8642788 -0.3036485 0.1990160 0.5056979 -0.7568838 0.0244163 0.1839238 0.1495869 0.6536796 0.9931883 0.9064707 0.0559880 0.5300197 -0.7686018 0.1613048 -1.4147986 -0.0989691 -0.5075848 0.8067585
Agathobaculum_butyriciproducens 0.5346760 0.0005963 0.0020908 0.8279723 0.0000002 0.0000594 0.9144912 0.0000385 0.0036425 0.7414533 0.0007497 0.0831380 -0.1730379 0.5716885 0.9826710 0.5265003 1.1294442 0.4879047 1.3410778 0.3153486 1.1675580
Akkermansia_muciniphila 0.2265332 0.5346338 0.6548793 0.4426396 0.2257864 0.5213278 0.2448765 0.6351576 0.8589750 0.6404028 0.2150693 0.7316337 0.3955263 0.5877058 0.9826710 -0.2762329 1.1615122 -0.7723372 1.2620901 -0.3756618 1.6564675
Alistipes_communis 1.4156089 0.0000002 0.0000022 -0.1459676 0.5792885 0.8025543 0.1392988 0.7083954 0.8924991 -0.4312340 0.2472697 0.7493886 -0.5705328 0.2792210 0.8436038 -0.6648179 0.3728827 -0.5948808 0.8734784 -1.1645844 0.3021163
Alistipes_finegoldii 1.5797872 0.0000000 0.0000003 0.0867226 0.7491813 0.8861676 -0.3083441 0.4221546 0.7400735 0.4817892 0.2099072 0.7316337 0.7901333 0.1465103 0.6639826 -0.4480011 0.6214462 -1.0649847 0.4482966 -0.2739968 1.2375752
Alistipes_ihumii 0.8177299 0.0005524 0.0020114 0.0088453 0.9696389 0.9834909 0.0171960 0.9582959 0.9973905 0.0004946 0.9987986 1.0000000 -0.0167014 0.9713358 0.9948202 -0.4493627 0.4670533 -0.6311741 0.6655660 -0.6471431 0.6481323
Alistipes_indistinctus 0.5482124 0.0204565 0.0489740 -0.1199680 0.6091625 0.8084213 -0.2452204 0.4603765 0.7709511 0.0052844 0.9872824 1.0000000 0.2505047 0.5935005 0.9826710 -0.5824283 0.3424923 -0.8996075 0.4091667 -0.6483636 0.6589323
Alistipes_onderdonkii 1.1563653 0.0023953 0.0073941 -0.3258552 0.3859757 0.7078181 0.1297417 0.8070748 0.9471457 -0.7814522 0.1421716 0.6749058 -0.9111939 0.2259812 0.7792030 -1.0660834 0.4143729 -0.9176903 1.1771738 -1.8277011 0.2647967
Alistipes_putredinis 0.9445127 0.0282302 0.0626357 -0.8463122 0.0489734 0.3082348 -0.7962487 0.1890307 0.5389703 -0.8963757 0.1390798 0.6749058 -0.1001269 0.9067293 0.9826710 -1.6887706 -0.0038538 -1.9883379 0.3958404 -2.0871183 0.2943670
Alistipes_senegalensis 0.9322196 0.0000170 0.0000945 0.1316225 0.5321203 0.7830163 -0.1766143 0.5535200 0.8080869 0.4398594 0.1407181 0.6749058 0.6164737 0.1445178 0.6639826 -0.2835038 0.5467489 -0.7640232 0.4107946 -0.1468861 1.0266048
Alistipes_shahii 1.4174456 0.0000021 0.0000148 0.1891343 0.5126785 0.7827994 0.2018996 0.6212851 0.8482931 0.1763690 0.6656796 0.9931883 -0.0255307 0.9647328 0.9948202 -0.3801017 0.7583703 -0.6035765 1.0073757 -0.6281973 0.9809352
Anaerobutyricum_hallii -1.8955964 0.0000000 0.0000000 -0.4257955 0.0499254 0.3082348 -0.5754616 0.0609899 0.3093058 -0.2761295 0.3661031 0.8507175 0.2993320 0.4884658 0.9826710 -0.8514507 -0.0001404 -1.1777689 0.0268457 -0.8777565 0.3254975
Anaerofilum_hominis -0.0089662 0.9737315 0.9806374 0.7155077 0.0093145 0.1151234 0.8841607 0.0228227 0.1839238 0.5468547 0.1566262 0.6950289 -0.3373060 0.5359045 0.9826710 0.1786396 1.2523758 0.1244856 1.6438358 -0.2119623 1.3056717
Anaeromassilibacillus_senegalensis 0.2107823 0.4104327 0.5429330 0.0351464 0.8907214 0.9582003 0.3295059 0.3632679 0.6934416 -0.2592130 0.4737669 0.9749986 -0.5887189 0.2508154 0.8073470 -0.4692168 0.5395096 -0.3841743 1.0431861 -0.9720871 0.4536611
Anaerostipes_hadrus -2.9248630 0.0000000 0.0000000 0.2033639 0.4001773 0.7078181 -0.2058624 0.5470525 0.8080869 0.6125902 0.0740811 0.6187951 0.8184526 0.0915378 0.5878263 -0.2727152 0.6794430 -0.8795203 0.4677955 -0.0603068 1.2854872
Anaerotignum_faecicola -0.7584214 0.0005088 0.0019012 -0.7661305 0.0004479 0.0198577 -1.1130716 0.0003178 0.0152257 -0.4191894 0.1672638 0.6963755 0.6938822 0.1065669 0.6176528 -1.1882964 -0.3439645 -1.7104417 -0.5157015 -1.0158847 0.1775060
Anaerotruncus_colihominis 0.0303582 0.8906679 0.9231740 0.4729027 0.0334735 0.2532106 0.3081960 0.3247486 0.6856880 0.6376095 0.0423922 0.4815749 0.3294135 0.4561767 0.9815046 0.0374663 0.9083392 -0.3079520 0.9243439 0.0221575 1.2530615
Anaerotruncus_massiliensis -0.3888396 0.0643297 0.1251344 0.2080020 0.3205611 0.6553058 0.4352922 0.1425392 0.4616646 -0.0192881 0.9479613 1.0000000 -0.4545802 0.2778800 0.8436038 -0.2042434 0.6202475 -0.1480403 1.0186246 -0.6019617 0.5633855
Anaerotruncus_rubiinfantis 0.4760658 0.0385038 0.0810006 -0.0114854 0.9599156 0.9832997 0.1040057 0.7477649 0.9153674 -0.1269766 0.6942994 0.9931883 -0.2309823 0.6134297 0.9826710 -0.4620554 0.4390846 -0.5335564 0.7415679 -0.7638186 0.5098654
Bacteroides_caccae -0.3561368 0.1462696 0.2371081 -0.3651931 0.1363479 0.4665397 -0.5059492 0.1446766 0.4616646 -0.2244370 0.5160331 0.9931883 0.2815122 0.5647575 0.9826710 -0.8469359 0.1165497 -1.1876213 0.1757228 -0.9053391 0.4564651
Bacteroides_cellulosilyticus -0.4363713 0.1264674 0.2088183 0.1506300 0.5966722 0.8025543 0.2192981 0.5861255 0.8281574 0.0819619 0.8385096 1.0000000 -0.1373362 0.8093017 0.9826710 -0.4103462 0.7116063 -0.5744903 1.0130866 -0.7109299 0.8748538
Bacteroides_clarus -0.2274338 0.4041730 0.5412435 0.1653956 0.5438823 0.7844941 -0.1587345 0.6804936 0.8835689 0.4895257 0.2046070 0.7316337 0.6482602 0.2350133 0.7852210 -0.3715817 0.7023729 -0.9185640 0.6010951 -0.2694456 1.2484970
Bacteroides_eggerthii 0.1342165 0.7043028 0.8065403 -0.2632158 0.4569892 0.7397360 -0.2007339 0.6883303 0.8835689 -0.3256977 0.5148498 0.9931883 -0.1249638 0.8597374 0.9826710 -0.9603402 0.4339086 -1.1871736 0.7857058 -1.3110232 0.6596278
Bacteroides_fragilis -0.0442056 0.8253848 0.8746372 0.0587498 0.7693722 0.8861676 -0.1164111 0.6814272 0.8835689 0.2339106 0.4092868 0.8873087 0.3503217 0.3825316 0.9699910 -0.3362753 0.4537748 -0.6753764 0.4425543 -0.3244234 0.7922446
Bacteroides_ovatus -0.8483739 0.0040157 0.0120047 0.4946195 0.0907409 0.3878452 0.3770543 0.3606477 0.6934416 0.6121847 0.1381472 0.6749058 0.2351303 0.6864079 0.9826710 -0.0793748 1.0686138 -0.4351548 1.1892635 -0.1991071 1.4234764
Bacteroides_stercoris -0.5632263 0.1575283 0.2527573 -0.1341134 0.7357061 0.8779013 -0.2682435 0.6333357 0.8589750 0.0000167 0.9999762 1.0000000 0.2682602 0.7356743 0.9826710 -0.9173595 0.6491327 -1.3765465 0.8400595 -1.1070344 1.1070679
Bacteroides_thetaiotaomicron -1.0299489 0.0004577 0.0017333 -0.0489703 0.8651458 0.9560366 -0.1904539 0.6407608 0.8624459 0.0925133 0.8204366 1.0000000 0.2829672 0.6237804 0.9826710 -0.6174830 0.5195424 -0.9949065 0.6139986 -0.7110306 0.8960572
Bacteroides_uniformis 0.3455271 0.2172031 0.3270814 -0.0748054 0.7888861 0.8998423 0.0128016 0.9741641 0.9973905 -0.1624123 0.6808984 0.9931883 -0.1752139 0.7538505 0.9826710 -0.6255846 0.4759739 -0.7665579 0.7921611 -0.9408915 0.6160668
Bacteroides_xylanisolvens -0.7462881 0.0039621 0.0119705 0.0278735 0.9131985 0.9605496 -0.0169806 0.9625687 0.9973905 0.0727275 0.8405286 1.0000000 0.0897081 0.8607607 0.9826710 -0.4762895 0.5320364 -0.7303774 0.6964163 -0.6398636 0.7853186
Barnesiella_intestinihominis -0.4560620 0.0482146 0.0971131 -0.5545883 0.0166022 0.1473444 -0.5434110 0.0956377 0.3994282 -0.5657657 0.0825192 0.6333906 -0.0223547 0.9611509 0.9948202 -1.0070272 -0.1021494 -1.1836176 0.0967957 -1.2052493 0.0737179
Bifidobacterium_adolescentis -0.6155977 0.0680443 0.1280893 -0.2758952 0.4115531 0.7078181 -0.4756708 0.3172963 0.6856880 -0.0761196 0.8725241 1.0000000 0.3995512 0.5519108 0.9826710 -0.9376476 0.3858573 -1.4120588 0.4607172 -1.0114499 0.8592107
Bifidobacterium_longum 0.6487073 0.0199337 0.0486526 -0.3362453 0.2247953 0.5213278 -0.0064432 0.9868547 0.9973905 -0.6660473 0.0896054 0.6432181 -0.6596041 0.2337645 0.7852210 -0.8811564 0.2086658 -0.7774993 0.7646128 -1.4362324 0.1041378
Bilophila_SGB15451 -0.7056271 0.0001804 0.0008007 -0.1597682 0.3866757 0.7078181 -0.0529905 0.8390344 0.9608298 -0.2665460 0.3071016 0.8001546 -0.2135555 0.5626444 0.9826710 -0.5232419 0.2037054 -0.5673102 0.4613292 -0.7802848 0.2471928
Bilophila_wadsworthia 1.3934528 0.0000000 0.0000002 -0.3725428 0.1129984 0.4222573 -0.4032276 0.2246579 0.5853472 -0.3418580 0.3024218 0.8001546 0.0613696 0.8957408 0.9826710 -0.8342112 0.0891256 -1.0564942 0.2500389 -0.9943867 0.3106706
Blautia_faecis -1.3614636 0.0000000 0.0000003 -0.0327953 0.8880960 0.9582003 -0.1349206 0.6825253 0.8835689 0.0693300 0.8333121 1.0000000 0.2042507 0.6613360 0.9826710 -0.4923064 0.4267158 -0.7851346 0.5152933 -0.5801495 0.7188095
Blautia_glucerasea -0.1263392 0.6164955 0.7295197 -0.2220832 0.3790482 0.7078181 -0.3455219 0.3335715 0.6856880 -0.0986445 0.7819821 1.0000000 0.2468774 0.6246052 0.9826710 -0.7192698 0.2751033 -1.0490471 0.3580033 -0.8013750 0.6040860
Blautia_massiliensis -1.4162505 0.0000006 0.0000047 -0.3821926 0.1625235 0.4843937 -0.8764856 0.0242862 0.1839238 0.1121003 0.7713074 1.0000000 0.9885859 0.0714443 0.5797192 -0.9201178 0.1557326 -1.6376565 -0.1153147 -0.6482108 0.8724114
Blautia_obeum -1.0121044 0.0000166 0.0000941 0.0993463 0.6635318 0.8325810 0.1907875 0.5549992 0.8080869 0.0079052 0.9804546 1.0000000 -0.1828824 0.6888303 0.9826710 -0.3507731 0.5494658 -0.4461371 0.8277122 -0.6283001 0.6441104
Blautia_sp_MCC283 -0.1466664 0.5567174 0.6736447 0.1836045 0.4620223 0.7397360 0.2746780 0.4368299 0.7573466 0.0925310 0.7929744 1.0000000 -0.1821470 0.7150581 0.9826710 -0.3081622 0.6753712 -0.4211780 0.9705341 -0.6025391 0.7876011
Blautia_wexlerae -2.3493073 0.0000000 0.0000000 -0.3448441 0.1521558 0.4779906 -0.5729456 0.0930832 0.3945616 -0.1167427 0.7308410 0.9931883 0.4562029 0.3426836 0.9442582 -0.8181563 0.1284680 -1.2426882 0.0967970 -0.7857288 0.5522435
Brotolimicola_acetigignens 0.1353203 0.6545573 0.7649970 0.5759606 0.0581651 0.3339497 0.7695106 0.0734858 0.3448326 0.3824107 0.3714401 0.8507175 -0.3870998 0.5223215 0.9826710 -0.0201513 1.1720725 -0.0739952 1.6130163 -0.4601423 1.2249637
Butyricimonas_faecihominis 0.4003576 0.0197970 0.0486526 0.0633033 0.7102821 0.8620518 0.0849810 0.7245134 0.9024640 0.0416255 0.8627695 1.0000000 -0.0433555 0.8987555 0.9826710 -0.2726166 0.3992231 -0.3903498 0.5603118 -0.4331684 0.5164194
Butyricimonas_virosa 0.0550661 0.7787735 0.8539447 0.3260133 0.0976624 0.4019728 0.6689249 0.0168192 0.1687600 -0.0168983 0.9513604 1.0000000 -0.6858232 0.0816199 0.5878263 -0.0604306 0.7124572 0.1221019 1.2157479 -0.5631036 0.5293070
Candidatus_Borkfalkia_ceftriaxoniphila 0.1986226 0.2564394 0.3754062 -0.0111994 0.9488780 0.9763818 -0.0013646 0.9955948 1.0000000 -0.0210341 0.9321048 1.0000000 -0.0196695 0.9551001 0.9948202 -0.3555968 0.3331981 -0.4886913 0.4859620 -0.5078103 0.4657421
Candidatus_Cibionibacter_quicibialis 1.1064434 0.0000178 0.0000973 -0.2220064 0.3761915 0.7078181 -0.6107258 0.0864062 0.3724833 0.1667130 0.6379484 0.9931883 0.7774388 0.1221975 0.6538840 -0.7160463 0.2720335 -1.3097984 0.0883468 -0.5315700 0.8649960
Clostridia_bacterium_UC5_1_1D1 -0.7611670 0.0006880 0.0023829 0.4231452 0.0561005 0.3319281 0.0549157 0.8601472 0.9732343 0.7913747 0.0118326 0.2375212 0.7364590 0.0959907 0.5926385 -0.0111411 0.8574315 -0.5596049 0.6694362 0.1775482 1.4052011
Clostridiaceae_bacterium -1.7388199 0.0000000 0.0000000 0.2981331 0.1420141 0.4692485 0.2590470 0.3662544 0.6934416 0.3372193 0.2394117 0.7493886 0.0781723 0.8468528 0.9826710 -0.1008643 0.6971305 -0.3055394 0.8236333 -0.2267293 0.9011679
Clostridiaceae_bacterium_AF18_31LB 0.4302731 0.0297953 0.0655959 0.0804644 0.6823850 0.8425971 0.2956365 0.2887107 0.6783679 -0.1347076 0.6279307 0.9931883 -0.4303441 0.2745940 0.8436038 -0.3071311 0.4680599 -0.2528160 0.8440890 -0.6825406 0.4131254
Clostridiaceae_bacterium_Marseille_Q4143 0.4967185 0.0234273 0.0545358 -0.0917692 0.6730603 0.8383734 -0.2951891 0.3380152 0.6856880 0.1116507 0.7164288 0.9931883 0.4068397 0.3501430 0.9442582 -0.5204648 0.3369264 -0.9017987 0.3114206 -0.4942738 0.7175751
Clostridiaceae_bacterium_Marseille_Q4145 -0.1230312 0.5843983 0.7027513 0.0095868 0.9659880 0.9832997 -0.0856504 0.7877779 0.9361043 0.1048240 0.7415409 0.9931883 0.1904744 0.6719426 0.9826710 -0.4336992 0.4528728 -0.7129056 0.5416049 -0.5217228 0.7313708
Clostridiales_bacterium 1.4379104 0.0000000 0.0000000 -0.1070684 0.6204678 0.8158003 -0.1380774 0.6517483 0.8689977 -0.0760593 0.8033985 1.0000000 0.0620182 0.8859223 0.9826710 -0.5332170 0.3190803 -0.7410831 0.4649282 -0.6783838 0.5262653
Clostridiales_bacterium_KLE1615 -1.2833221 0.0000000 0.0000004 -0.1689414 0.4449112 0.7303745 -0.0054629 0.9860593 0.9973905 -0.3324199 0.2879676 0.7788837 -0.3269571 0.4597452 0.9815046 -0.6045804 0.2666977 -0.6218976 0.6109718 -0.9481583 0.2833185
Clostridium_SGB4750 -1.3663630 0.0000000 0.0000001 -0.2465903 0.2618133 0.5719615 -0.2933415 0.3452246 0.6904493 -0.1998391 0.5194270 0.9931883 0.0935024 0.8312157 0.9826710 -0.6790305 0.1858500 -0.9052499 0.3185669 -0.8110563 0.4113782
Clostridium_SGB4909 -0.3000268 0.2865312 0.4151778 0.0499601 0.8589011 0.9528434 0.2804109 0.4810368 0.7851405 -0.1804906 0.6496372 0.9931883 -0.4609015 0.4126712 0.9815046 -0.5041173 0.6040375 -0.5036156 1.0644373 -0.9636315 0.6026503
Clostridium_fessum -0.6882767 0.0002905 0.0012456 -0.7462469 0.0000903 0.0064196 -0.7461517 0.0051223 0.0909210 -0.7463421 0.0050625 0.1198134 -0.0001904 0.9995919 0.9995919 -1.1131698 -0.3793240 -1.2653522 -0.2269512 -1.2649561 -0.2277280
Clostridium_leptum -0.2791866 0.2118559 0.3234789 0.2877047 0.1983110 0.5056979 0.7062355 0.0264013 0.1874496 -0.1308261 0.6782847 0.9931883 -0.8370616 0.0620375 0.5505824 -0.1521404 0.7275498 0.0838492 1.3286218 -0.7525094 0.4908572
Clostridium_sp_AF20_17LB 0.7819860 0.0016161 0.0051571 0.4186926 0.0878674 0.3878452 0.5949273 0.0865630 0.3724833 0.2424579 0.4827446 0.9833147 -0.3524694 0.4708655 0.9826710 -0.0628093 0.9001945 -0.0864039 1.2762585 -0.4381037 0.9230195
Clostridium_sp_AF27_2AA -0.1956906 0.3219920 0.4516249 0.1962029 0.3207307 0.6553058 0.7511658 0.0077848 0.1196466 -0.3587601 0.1994002 0.7316337 -1.1099260 0.0054470 0.2087999 -0.1927941 0.5851998 0.2007303 1.3016014 -0.9085740 0.1910537
Clostridium_sp_AF36_4 -0.5008631 0.0683607 0.1280893 -0.0448974 0.8695609 0.9571910 -0.2524275 0.5143464 0.8070408 0.1626328 0.6739313 0.9931883 0.4150603 0.4482014 0.9815046 -0.5839373 0.4941425 -1.0151757 0.5103207 -0.5992539 0.9245194
Clostridium_sp_AM22_11AC -1.4668820 0.0000000 0.0000000 -0.1321066 0.5124007 0.7827994 -0.0862622 0.7622988 0.9212462 -0.1779511 0.5323834 0.9931883 -0.0916889 0.8200575 0.9826710 -0.5294447 0.2652315 -0.6485005 0.4759762 -0.7395543 0.3836522
Clostridium_sp_AM33_3 -0.1177008 0.5146238 0.6410226 0.0556913 0.7577065 0.8861676 0.1882424 0.4614848 0.7709511 -0.0768598 0.7632421 0.9943154 -0.2651022 0.4631043 0.9815046 -0.3001947 0.4115772 -0.3153407 0.6918254 -0.5798740 0.4261544
Collinsella_aerofaciens 0.1446952 0.4115483 0.5429330 -0.5620412 0.0016648 0.0429828 -0.6677641 0.0080045 0.1196466 -0.4563182 0.0680468 0.6187951 0.2114459 0.5483137 0.9826710 -0.9090984 -0.2149840 -1.1588544 -0.1766738 -0.9468539 0.0342174
Coprobacter_fastidiosus -0.0506822 0.8212646 0.8743250 0.3837940 0.0885220 0.3878452 0.3324306 0.2957771 0.6832163 0.4351574 0.1711517 0.6963755 0.1027268 0.8189040 0.9826710 -0.0584917 0.8260797 -0.2934091 0.9582704 -0.1899755 1.0602903
Coprococcus_catus -0.9650382 0.0000053 0.0000339 0.0223985 0.9130541 0.9605496 -0.0625851 0.8293030 0.9582446 0.1073821 0.7111736 0.9931883 0.1699672 0.6787485 0.9826710 -0.3820600 0.4268570 -0.6348990 0.5097288 -0.4642853 0.6790495
Coprococcus_comes -1.2165824 0.0000000 0.0000004 -0.5434396 0.0104765 0.1167873 -0.8905865 0.0031322 0.0684256 -0.1962927 0.5090084 0.9931883 0.6942938 0.0999849 0.6041638 -0.9578021 -0.1290771 -1.4769146 -0.3042584 -0.7819585 0.3893731
Coprococcus_eutactus -0.5007188 0.0685548 0.1280893 -0.2139178 0.4345741 0.7255890 -0.2427976 0.5306755 0.8080869 -0.1850380 0.6323053 0.9931883 0.0577596 0.9159087 0.9826710 -0.7531849 0.3253493 -1.0058672 0.5202721 -0.9472457 0.5771698
Dorea_formicigenerans -1.4562886 0.0000000 0.0000000 -0.2245237 0.2239555 0.5213278 -0.6718095 0.0107270 0.1409286 0.2227621 0.3927603 0.8782987 0.8945716 0.0161087 0.3267763 -0.5877197 0.1386723 -1.1857364 -0.1578826 -0.2905843 0.7361085
Dorea_longicatena -2.2712591 0.0000000 0.0000000 -0.1107162 0.5851809 0.8025543 -0.4694052 0.1032111 0.4022204 0.2479727 0.3874054 0.8782484 0.7173779 0.0782928 0.5878263 -0.5104639 0.2890314 -1.0350530 0.0962427 -0.3170363 0.8129817
Dorea_sp_AF36_15AT -0.0577438 0.8064769 0.8708724 -0.0610864 0.7955183 0.9001083 -0.5172080 0.1223251 0.4342541 0.3950352 0.2367074 0.7493886 0.9122432 0.0543339 0.5300197 -0.5257945 0.4036216 -1.1747758 0.1403597 -0.2617898 1.0518601
Dysosmobacter_SGB15077 -0.4603851 0.0560121 0.1104683 0.3690354 0.1248192 0.4487171 0.5565276 0.1020534 0.4022204 0.1815431 0.5920122 0.9931883 -0.3749844 0.4342674 0.9815046 -0.1032994 0.8413701 -0.1118319 1.2248871 -0.4860614 0.8491477
Dysosmobacter_welbionis 1.8572849 0.0000000 0.0000000 -0.6159446 0.0043220 0.0876758 -0.5988990 0.0483940 0.2545166 -0.6329902 0.0368773 0.4363818 -0.0340911 0.9362563 0.9848029 -1.0361688 -0.1957204 -1.1935215 -0.0042766 -1.2269410 -0.0390393
Eggerthella_lenta -0.7121128 0.0046215 0.0133930 -0.0442070 0.8587064 0.9528434 0.2936938 0.4037380 0.7234323 -0.3821077 0.2771533 0.7716817 -0.6758015 0.1748081 0.7280069 -0.5337969 0.4453829 -0.3990821 0.9864696 -1.0741010 0.3098856
Enterocloster_citroniae -0.3924227 0.0826290 0.1475889 -0.0327327 0.8843597 0.9582003 -0.0517634 0.8708761 0.9814636 -0.0137020 0.9656404 1.0000000 0.0380614 0.9326087 0.9846129 -0.4764472 0.4109819 -0.6796250 0.5760982 -0.6408544 0.6134505
Enterocloster_hominis -0.5869120 0.0005802 0.0020597 -0.4231029 0.0123460 0.1252238 -0.6760690 0.0048314 0.0909210 -0.1701368 0.4726187 0.9749986 0.5059322 0.1322529 0.6639826 -0.7532869 -0.0929189 -1.1432835 -0.2088545 -0.6368235 0.2965500
Escherichia_coli 0.1013471 0.6957599 0.8032351 -0.8303378 0.0016028 0.0429828 -0.7921934 0.0319261 0.2108606 -0.8684823 0.0187127 0.2952455 -0.0762888 0.8829654 0.9826710 -1.3412078 -0.3194679 -1.5150808 -0.0693061 -1.5905531 -0.1464114
Eubacterium_ramulus -0.3537106 0.0931463 0.1613021 -0.4957961 0.0190916 0.1643034 -0.8524856 0.0045590 0.0909210 -0.1391066 0.6390195 0.9931883 0.7133790 0.0904467 0.5878263 -0.9093452 -0.0822470 -1.4376628 -0.2673085 -0.7236228 0.4454096
Eubacterium_rectale -0.8886340 0.0055440 0.0154364 0.0102462 0.9741811 0.9840937 0.4783100 0.2864924 0.6783679 -0.4578176 0.3070255 0.8001546 -0.9361276 0.1406125 0.6639826 -0.6139550 0.6344474 -0.4049425 1.3615625 -1.3400724 0.4244373
Eubacterium_siraeum -0.0845427 0.7570292 0.8431227 -0.3587257 0.1903749 0.4996872 -0.2763885 0.4750186 0.7797994 -0.4410628 0.2543528 0.7568859 -0.1646743 0.7631739 0.9826710 -0.8974267 0.1799754 -1.0386572 0.4858802 -1.2024705 0.3203449
Eubacterium_ventriosum -1.2106706 0.0000002 0.0000017 0.2183481 0.3268933 0.6631265 -0.0614242 0.8452471 0.9616687 0.4981205 0.1144179 0.6732760 0.5595446 0.2094812 0.7678898 -0.2201206 0.6568168 -0.6818629 0.5590145 -0.1216174 1.1178583
Faecalibacterium_SGB15346 1.1035100 0.0014443 0.0047695 0.2623097 0.4421378 0.7300415 0.0108100 0.9821250 0.9973905 0.5138093 0.2872112 0.7788837 0.5029992 0.4611416 0.9815046 -0.4099823 0.9346016 -0.9404914 0.9621115 -0.4364177 1.4640362
Faecalibacterium_prausnitzii 1.5436646 0.0000000 0.0000000 -0.1207767 0.5305277 0.7830163 -0.2416882 0.3753748 0.7060028 0.0001347 0.9996048 1.0000000 0.2418229 0.5300698 0.9826710 -0.5002199 0.2586664 -0.7786050 0.2952287 -0.5361756 0.5364451
Faecalibacterium_sp_CLA_AA_H233 0.1236805 0.7161661 0.8135647 0.4635346 0.1741299 0.4901612 0.6135445 0.2034695 0.5556282 0.3135248 0.5145312 0.9931883 -0.3000196 0.6592521 0.9826710 -0.2070259 1.1340952 -0.3353071 1.5623960 -0.6342550 1.2613047
Faecalibacterium_sp_HTFF 0.5028578 0.0964252 0.1649684 0.4804993 0.1120361 0.4222573 0.4834863 0.2575521 0.6305585 0.4775123 0.2629182 0.7619261 -0.0059740 0.9920873 0.9955929 -0.1133480 1.0743466 -0.3568151 1.3237876 -0.3618399 1.3168645
Faecalicatena_fissicatena -0.2777654 0.2390199 0.3554012 -0.1554422 0.5093267 0.7827994 -0.2001755 0.5480919 0.8080869 -0.1107089 0.7393730 0.9931883 0.0894666 0.8492934 0.9826710 -0.6195741 0.3086897 -0.8569280 0.4565770 -0.7667196 0.5453017
Flavonifractor_plautii 0.8963234 0.0008370 0.0028298 -0.4168995 0.1153073 0.4252894 -0.0145324 0.9689355 0.9973905 -0.8192666 0.0291275 0.3617661 -0.8047341 0.1284399 0.6632169 -0.9368686 0.1030696 -0.7502952 0.7212303 -1.5541983 -0.0843349
Fusicatenibacter_saccharivorans -0.2990210 0.1665937 0.2643162 -0.2625046 0.2243148 0.5213278 -0.3975887 0.1935253 0.5389703 -0.1274205 0.6758370 0.9931883 0.2701682 0.5310819 0.9826710 -0.6874706 0.1624613 -0.9989209 0.2037434 -0.7280735 0.4732324
Fusicatenibacter_sp_CLA_AA_H277 0.2463429 0.2083592 0.3215979 -0.1194072 0.5412232 0.7844941 -0.2690954 0.3309610 0.6856880 0.0302810 0.9126630 1.0000000 0.2993764 0.4438853 0.9815046 -0.5045292 0.2657148 -0.8140478 0.2758570 -0.5140559 0.5746179
GGB13404_SGB14252 1.1032425 0.0000002 0.0000018 0.0979484 0.6302021 0.8165266 0.1683017 0.5588687 0.8080869 0.0275951 0.9235227 1.0000000 -0.1407066 0.7294441 0.9826710 -0.3030398 0.4989366 -0.3991016 0.7357050 -0.5391673 0.5943575
GGB1420_SGB1957 0.3443263 0.0243489 0.0557669 -0.1723725 0.2568791 0.5655322 -0.1955711 0.3629562 0.6934416 -0.1491738 0.4870092 0.9833147 0.0463973 0.8784851 0.9826710 -0.4715315 0.1267865 -0.6188848 0.2277426 -0.5720094 0.2736617
GGB2653_SGB3574 -0.5695842 0.0044208 0.0130783 0.5521852 0.0057526 0.0961022 0.6718270 0.0172325 0.1687600 0.4325435 0.1228250 0.6749058 -0.2392836 0.5450906 0.9826710 0.1625840 0.9417865 0.1205364 1.2231176 -0.1181244 0.9832113
GGB2998_SGB3988 0.7425379 0.0001167 0.0005714 -0.0138126 0.9415278 0.9749077 0.3797782 0.1553699 0.4848906 -0.4074035 0.1272180 0.6749058 -0.7871817 0.0378758 0.5122248 -0.3850982 0.3574730 -0.1455955 0.9051520 -0.9321838 0.1173768
GGB3034_SGB4030 -1.0115509 0.0000000 0.0000000 0.4015157 0.0136740 0.1339112 0.0842006 0.7122698 0.8924991 0.7188307 0.0018973 0.0831380 0.6346300 0.0505259 0.5300197 0.0834651 0.7195662 -0.3658449 0.5342462 0.2692935 1.1683678
GGB3109_SGB4121 -0.8855511 0.0000010 0.0000073 -0.1906146 0.2741980 0.5855055 -0.6517931 0.0088136 0.1251536 0.2705638 0.2721688 0.7655571 0.9223569 0.0087346 0.2609051 -0.5336898 0.1524606 -1.1372488 -0.1663373 -0.2143436 0.7554712
GGB3175_SGB4191 0.6599143 0.0131748 0.0346450 -0.2495102 0.3446713 0.6845220 -0.0396215 0.9154292 0.9973905 -0.4593988 0.2187703 0.7316337 -0.4197773 0.4264756 0.9815046 -0.7693885 0.2703681 -0.7752558 0.6960128 -1.1942022 0.2754045
GGB33469_SGB15236 0.6125204 0.0443114 0.0911916 -0.2412381 0.4258720 0.7242374 -0.3278914 0.4443148 0.7601531 -0.1545847 0.7178845 0.9931883 0.1733067 0.7746723 0.9826710 -0.8379858 0.3555096 -1.1722969 0.5165140 -0.9980364 0.6888669
GGB33512_SGB15203 0.4893351 0.0056008 0.0154429 -0.1850376 0.2899263 0.6144707 0.2243406 0.3643163 0.6934416 -0.5944159 0.0169308 0.2897371 -0.8187565 0.0200286 0.3378885 -0.5291811 0.1591059 -0.2626267 0.7113079 -1.0808332 -0.1079986
GGB33586_SGB53517 0.4509516 0.0200435 0.0486526 -0.3512535 0.0691663 0.3507721 -0.0999710 0.7133708 0.8924991 -0.6025360 0.0277831 0.3617661 -0.5025650 0.1924602 0.7386309 -0.7303920 0.0278850 -0.6364568 0.4365147 -1.1384158 -0.0666563
GGB3537_SGB4727 -0.0453741 0.8183308 0.8743250 0.4219867 0.0338803 0.2532106 0.3930352 0.1609390 0.4968117 0.4509382 0.1076776 0.6732760 0.0579030 0.8834752 0.9826710 0.0325290 0.8114443 -0.1580523 0.9441226 -0.0995268 1.0014031
GGB38744_SGB14842 -0.5974362 0.0055236 0.0154364 0.8076923 0.0002027 0.0115115 0.7386103 0.0150524 0.1687600 0.8767742 0.0039961 0.1031732 0.1381639 0.7454391 0.9826710 0.3882226 1.2271619 0.1450555 1.3321651 0.2838899 1.4696586
GGB45432_SGB63101 -0.0714864 0.7617945 0.8451158 0.4846980 0.0411204 0.2715858 1.1418554 0.0007723 0.0313313 -0.1724594 0.6049841 0.9931883 -1.3143148 0.0058817 0.2087999 0.0197821 0.9496139 0.4839936 1.7997172 -0.8295781 0.4846594
GGB45613_SGB63326 -0.3369888 0.2098499 0.3221480 0.4975471 0.0648674 0.3349516 0.6182769 0.1045389 0.4022204 0.3768173 0.3207308 0.8206087 -0.2414596 0.6525628 0.9826710 -0.0310229 1.0261171 -0.1296562 1.3662100 -0.3702710 1.1239056
GGB47687_SGB2286 0.6535481 0.0054666 0.0154364 -0.0697142 0.7642679 0.8861676 0.0494591 0.8804733 0.9871353 -0.1888876 0.5655310 0.9931883 -0.2383467 0.6083037 0.9826710 -0.5280104 0.3885820 -0.5990357 0.6979539 -0.8366499 0.4588748
GGB52106_SGB72838 -0.3682983 0.0279506 0.0625036 0.2083783 0.2113309 0.5213278 0.2027371 0.3895107 0.7153866 0.2140196 0.3631926 0.8507175 0.0112825 0.9729411 0.9948202 -0.1195328 0.5362895 -0.2612613 0.6667354 -0.2494547 0.6774938
GGB52130_SGB14966 0.4437215 0.0187024 0.0474239 -0.1670068 0.3726365 0.7078181 -0.2279067 0.3898489 0.7153866 -0.1061068 0.6883078 0.9931883 0.1217999 0.7448375 0.9826710 -0.5358914 0.2018779 -0.7498831 0.2940697 -0.6274936 0.4152800
GGB9062_SGB13981 -0.0647434 0.6986418 0.8032966 0.2382218 0.1554877 0.4779906 0.0747668 0.7520113 0.9166147 0.4016769 0.0905941 0.6432181 0.3269101 0.3289556 0.9442582 -0.0914217 0.5678653 -0.3916829 0.5412164 -0.0642459 0.8675997
GGB9063_SGB13982 0.2916340 0.0454358 0.0928328 0.0315966 0.8273630 0.9250831 -0.0077536 0.9698285 0.9973905 0.0709469 0.7290290 0.9931883 0.0787005 0.7859369 0.9826710 -0.2540426 0.3172359 -0.4119367 0.3964295 -0.3327797 0.4746735
GGB9064_SGB13983 0.8601846 0.0000099 0.0000613 0.0663380 0.7253868 0.8729231 0.4892562 0.0684844 0.3353373 -0.3565802 0.1827094 0.7225423 -0.8458365 0.0262335 0.3921212 -0.3059460 0.4386219 -0.0375302 1.0160426 -0.8827717 0.1696112
GGB9342_SGB14306 0.5828192 0.0260252 0.0591292 0.2022035 0.4368863 0.7255890 -0.1239011 0.7361721 0.9093663 0.5283081 0.1515889 0.6943751 0.6522092 0.2105748 0.7678898 -0.3101122 0.7145192 -0.8488343 0.6010320 -0.1958062 1.2524224
GGB9345_SGB14311 0.5748965 0.0274892 0.0619598 -0.0285100 0.9122907 0.9605496 -0.0758206 0.8360018 0.9608298 0.0188006 0.9590133 1.0000000 0.0946211 0.8549703 0.9826710 -0.5388273 0.4818073 -0.7979259 0.6462848 -0.7024892 0.7400903
GGB9453_SGB14844 -0.1193012 0.5063901 0.6335453 0.0858262 0.6325206 0.8165266 0.3475716 0.1722283 0.5128561 -0.1759191 0.4881950 0.9833147 -0.5234907 0.1459284 0.6639826 -0.2679327 0.4395852 -0.1530017 0.8481449 -0.6759270 0.3240888
GGB9502_SGB14899 0.2233381 0.0723169 0.1325734 -0.1985993 0.1096613 0.4222573 -0.3506347 0.0464103 0.2510951 -0.0465638 0.7899383 1.0000000 0.3040708 0.2199544 0.7792030 -0.4424067 0.0452082 -0.6956253 -0.0056441 -0.3911648 0.2980371
GGB9509_SGB14906 0.3914056 0.0206932 0.0489740 -0.2843912 0.0914987 0.3878452 0.0004460 0.9985010 1.0000000 -0.5692284 0.0173434 0.2897371 -0.5696744 0.0909958 0.5878263 -0.6152014 0.0464190 -0.4676545 0.4685466 -1.0368002 -0.1016565
GGB9522_SGB14921 0.3323671 0.0911204 0.1597419 0.2714537 0.1670022 0.4889550 0.3127595 0.2600291 0.6311817 0.2301479 0.4062564 0.8873087 -0.0826116 0.8329767 0.9826710 -0.1147078 0.6576153 -0.2336638 0.8591829 -0.3156583 0.7759541
GGB9531_SGB14932 0.0500117 0.7529563 0.8431227 0.0839896 0.5971995 0.8025543 0.1688978 0.4528644 0.7701406 -0.0009187 0.9967357 1.0000000 -0.1698165 0.5931984 0.9826710 -0.2292545 0.3972336 -0.2743465 0.6121421 -0.4436623 0.4418250
GGB9534_SGB14937 0.8954681 0.0001310 0.0006199 -0.0032018 0.9888375 0.9888375 0.0384368 0.9055195 0.9973905 -0.0448403 0.8897493 1.0000000 -0.0832771 0.8556334 0.9826710 -0.4544238 0.4480203 -0.6000481 0.6769216 -0.6826040 0.5929233
GGB9602_SGB15031 0.5413714 0.0404626 0.0838788 -0.6005399 0.0232335 0.1940679 -0.8628812 0.0212214 0.1795889 -0.3381987 0.3626274 0.8507175 0.5246825 0.3183471 0.9416957 -1.1181013 -0.0829786 -1.5952369 -0.1305255 -1.0697272 0.3933298
GGB9614_SGB15049 1.9494046 0.0000000 0.0000000 0.3478852 0.0767216 0.3718112 0.5883006 0.0347708 0.2244297 0.1074698 0.6975278 0.9931883 -0.4808308 0.2200769 0.7792030 -0.0377532 0.7335236 0.0426174 1.1339837 -0.4375970 0.6525366
GGB9619_SGB15067 0.6139043 0.0005773 0.0020597 0.1046523 0.5502642 0.7844941 0.1308535 0.5975550 0.8329130 0.0784512 0.7512805 0.9931883 -0.0524023 0.8810519 0.9826710 -0.2405742 0.4498789 -0.3576464 0.6193533 -0.4094969 0.5663992
GGB9621_SGB15073 0.6212828 0.0001452 0.0006651 -0.1927023 0.2291727 0.5248794 -0.1744520 0.4410959 0.7592196 -0.2109526 0.3512442 0.8507175 -0.0365006 0.9091287 0.9826710 -0.5079606 0.1225560 -0.6205465 0.2716424 -0.6565432 0.2346380
GGB9635_SGB15106 -0.0057553 0.9873382 0.9873382 -0.4155704 0.2527923 0.5608830 -0.7571623 0.1414123 0.4616646 -0.0739785 0.8852473 1.0000000 0.6831838 0.3468942 0.9442582 -1.1306067 0.2994658 -1.7689476 0.2546229 -1.0846209 0.9366639
GGB9646_SGB15123 0.4115811 0.0664366 0.1269839 0.1526647 0.4940478 0.7794976 0.1891696 0.5491896 0.8080869 0.1161599 0.7126163 0.9931883 -0.0730097 0.8700140 0.9826710 -0.2871560 0.5924855 -0.4331823 0.8115215 -0.5054890 0.7378088
GGB9667_SGB15164 0.9218116 0.0000250 0.0001339 0.0842555 0.6921111 0.8509071 0.3723322 0.2171768 0.5771735 -0.2038213 0.4981323 0.9892978 -0.5761535 0.1768749 0.7280069 -0.3351565 0.5036674 -0.2211410 0.9658054 -0.7966242 0.3889815
GGB9699_SGB15216 2.0745480 0.0000000 0.0000000 -0.1299469 0.5355669 0.7840258 -0.2859959 0.3356535 0.6856880 0.0261021 0.9298006 1.0000000 0.3120979 0.4570103 0.9815046 -0.5432605 0.2833667 -0.8708397 0.2988480 -0.5580812 0.6102853
GGB9708_SGB15234 1.4964436 0.0000006 0.0000047 -0.2131083 0.4595041 0.7397360 -0.2484536 0.5421344 0.8080869 -0.1777631 0.6622835 0.9931883 0.0706905 0.9022824 0.9826710 -0.7806959 0.3544792 -1.0515971 0.5546899 -0.9799994 0.6244732
GGB9715_SGB15265 -0.2027302 0.5574173 0.6736447 -0.1578396 0.6477654 0.8286728 -0.2862919 0.5582051 0.8080869 -0.0293874 0.9519954 1.0000000 0.2569044 0.7100067 0.9826710 -0.8387951 0.5231158 -1.2498523 0.6772686 -0.9918595 0.9330847
GGB9719_SGB15272 0.1118734 0.5213415 0.6465545 0.1278768 0.4636374 0.7397360 0.2378353 0.3356996 0.6856880 0.0179182 0.9420336 1.0000000 -0.2199171 0.5284876 0.9826710 -0.2158693 0.4716228 -0.2485697 0.7242403 -0.4679373 0.5037738
GGB9719_SGB15273 -0.1300549 0.3512375 0.4865924 0.1139982 0.4137246 0.7078181 0.4164334 0.0359143 0.2266593 -0.1884370 0.3393083 0.8507175 -0.6048705 0.0311543 0.4423904 -0.1607101 0.3887065 0.0277178 0.8051491 -0.5767136 0.1998396
GGB9730_SGB15291 0.9232657 0.0000005 0.0000041 -0.2808796 0.1121504 0.4222573 -0.5017567 0.0454010 0.2510951 -0.0600025 0.8095393 1.0000000 0.4417542 0.2108993 0.7678898 -0.6281292 0.0663699 -0.9931192 -0.0103942 -0.5508100 0.4308049
GGB9758_SGB15368 0.0288709 0.9459579 0.9663743 0.1249628 0.7692528 0.8861676 -0.0130693 0.9826993 0.9973905 0.2629950 0.6623047 0.9931883 0.2760642 0.7459204 0.9826710 -0.7148216 0.9647473 -1.2013748 1.1752362 -0.9239683 1.4499582
GGB9760_SGB15373 0.7472873 0.0000399 0.0002058 -0.1789817 0.3131413 0.6491396 -0.2576334 0.3048875 0.6856880 -0.1003301 0.6887420 0.9931883 0.1573033 0.6571834 0.9826710 -0.5282970 0.1703335 -0.7519188 0.2366520 -0.5940572 0.3933971
GGB9765_SGB15382 -0.0034039 0.9861196 0.9873382 0.3235198 0.0996440 0.4042698 0.4258812 0.1253520 0.4395057 0.2211584 0.4243277 0.8926598 -0.2047228 0.6010098 0.9826710 -0.0622494 0.7092890 -0.1199871 0.9717494 -0.3240933 0.7664101
GGB9770_SGB15390 0.0444962 0.8158030 0.8743250 -0.0153624 0.9358944 0.9749077 0.2829774 0.2959000 0.6832163 -0.3137022 0.2462056 0.7493886 -0.5966796 0.1196721 0.6535935 -0.3919487 0.3612239 -0.2498969 0.8158518 -0.8459746 0.2185702
GGB9775_SGB15395 0.4983309 0.0001018 0.0005074 -0.3049544 0.0158256 0.1449832 -0.0498971 0.7783201 0.9287518 -0.5600118 0.0018331 0.0831380 -0.5101147 0.0430179 0.5300197 -0.5519016 -0.0580073 -0.3993304 0.2995362 -0.9090504 -0.2109732
GGB9781_SGB15402 -0.5706066 0.0060151 0.0162694 0.4307636 0.0371508 0.2637708 0.5214751 0.0740662 0.3448326 0.3400521 0.2422440 0.7493886 -0.1814230 0.6586997 0.9826710 0.0259741 0.8355531 -0.0513071 1.0942573 -0.2320831 0.9121873
GGB9818_SGB15459 0.8201161 0.0000124 0.0000735 0.0240609 0.8949116 0.9590750 0.4515096 0.0812358 0.3662056 -0.4033878 0.1185345 0.6732760 -0.8548975 0.0199610 0.3378885 -0.3350745 0.3831963 -0.0566715 0.9596907 -0.9109949 0.1042193
Gemmiger_formicilis 0.8442966 0.0021758 0.0067903 0.1020173 0.7071175 0.8618943 -0.3691204 0.3372615 0.6856880 0.5731551 0.1365649 0.6749058 0.9422755 0.0840648 0.5878263 -0.4332089 0.6372435 -1.1264722 0.3882313 -0.1833412 1.3296514
Guopingia_tenuis -0.1581201 0.5011133 0.6297176 0.8256167 0.0005594 0.0198577 1.5390110 0.0000072 0.0010247 0.1122224 0.7353746 0.9931883 -1.4267886 0.0027419 0.1510606 0.3625212 1.2887122 0.8837251 2.1942970 -0.5423234 0.7667682
Holdemania_filiformis 0.0658600 0.7466674 0.8431227 -0.2959396 0.1478727 0.4772256 -0.1060722 0.7131243 0.8924991 -0.4858070 0.0931919 0.6455242 -0.3797348 0.3522759 0.9442582 -0.6978547 0.1059756 -0.6747871 0.4626428 -1.0538795 0.0822656
Hydrogenoanaerobacterium_saccharovorans 1.0835949 0.0000000 0.0000000 -0.5787780 0.0005027 0.0198577 -0.4208769 0.0698632 0.3362905 -0.7366790 0.0016659 0.0831380 -0.3158021 0.3341033 0.9442582 -0.9006389 -0.2569171 -0.8763142 0.0345603 -1.1916018 -0.2817562
Intestinimonas_butyriciproducens 0.2982007 0.2134420 0.3241579 0.1792461 0.4538593 0.7397360 0.4333247 0.2014238 0.5553821 -0.0748325 0.8247740 1.0000000 -0.5081572 0.2887972 0.8633515 -0.2921948 0.6506869 -0.2337700 1.1004193 -0.7411737 0.5915086
Intestinimonas_gabonensis 0.0179885 0.9290781 0.9525566 -0.0589087 0.7707161 0.8861676 -0.0953425 0.7388845 0.9093663 -0.0224750 0.9372893 1.0000000 0.0728675 0.8569462 0.9826710 -0.4573922 0.3395748 -0.6592016 0.4685167 -0.5856972 0.5407473
Intestinimonas_massiliensis 0.1847850 0.4059326 0.5412435 0.4164577 0.0621889 0.3339497 0.6369241 0.0440224 0.2500470 0.1959913 0.5326674 0.9931883 -0.4409327 0.3216355 0.9416957 -0.0214653 0.8543807 0.0172575 1.2565906 -0.4229753 0.8149579
Lachnoclostridium_sp_An138 -0.7915945 0.0004484 0.0017208 0.6184502 0.0057395 0.0961022 0.5053205 0.1079200 0.4086571 0.7315799 0.0203433 0.3040793 0.2262594 0.6092738 0.9826710 0.1822150 1.0546855 -0.1119578 1.1225989 0.1149988 1.3481610
Lachnospira_eligens -1.4168327 0.0000006 0.0000047 -0.1412929 0.6038984 0.8051978 -0.2333469 0.5448986 0.8080869 -0.0492388 0.8981769 1.0000000 0.1841080 0.7352974 0.9826710 -0.6780422 0.3954565 -0.9928540 0.5261602 -0.8078880 0.7094104
Lachnospira_pectinoschiza -1.0804390 0.0002182 0.0009532 -0.2348543 0.4121834 0.7078181 0.3417383 0.3990922 0.7225024 -0.8114469 0.0461094 0.4850025 -1.1531851 0.0451849 0.5300197 -0.7989291 0.3292205 -0.4564346 1.1399111 -1.6087182 -0.0141756
Lachnospiraceae_bacterium 0.2285355 0.4203803 0.5501751 0.7566681 0.0082483 0.1151234 0.3447218 0.3904399 0.7153866 1.1686145 0.0039685 0.1031732 0.8238927 0.1472919 0.6639826 0.1980115 1.3153248 -0.4457844 1.1352280 0.3790012 1.9582277
Lachnospiraceae_bacterium_AM48_27BH -0.6473736 0.0019343 0.0061036 0.1894153 0.3578208 0.6964919 0.5067397 0.0831505 0.3689804 -0.1279090 0.6601087 0.9931883 -0.6346488 0.1243301 0.6538840 -0.2162028 0.5950335 -0.0672151 1.0806945 -0.7012155 0.4453974
Lachnospiraceae_bacterium_CLA_AA_H215 0.3468883 0.1106220 0.1858899 -0.5685693 0.0093790 0.1151234 -0.4650551 0.1304917 0.4465018 -0.6720834 0.0292980 0.3617661 -0.2070283 0.6327976 0.9826710 -0.9955821 -0.1415565 -1.0692836 0.1391733 -1.2756294 -0.0685374
Lachnospiraceae_bacterium_CLA_AA_H244 0.6309932 0.0045727 0.0133880 -0.3810603 0.0843418 0.3863401 -0.4557307 0.1440873 0.4616646 -0.3063899 0.3246504 0.8232206 0.1493407 0.7340619 0.9826710 -0.8143463 0.0522257 -1.0688358 0.1573744 -0.9188025 0.3060226
Lachnotalea_sp_AF33_28 -0.2781623 0.3173061 0.4483330 0.2851886 0.3052744 0.6374848 0.3315267 0.3994116 0.7225024 0.2388505 0.5431107 0.9931883 -0.0926761 0.8674969 0.9826710 -0.2624025 0.8327797 -0.4433216 1.1063749 -0.5351225 1.0128236
Lacrimispora_amygdalina 0.2216610 0.3244496 0.4516848 0.2889599 0.1994301 0.5056979 0.5894038 0.0650857 0.3242866 -0.0114841 0.9711446 1.0000000 -0.6008878 0.1822369 0.7379384 -0.1539120 0.7318317 -0.0372655 1.2160730 -0.6374455 0.6144773
Lawsonibacter_SGB15145 1.3597684 0.0000000 0.0000000 -0.1811939 0.3596731 0.6964919 -0.2173220 0.4373410 0.7573466 -0.1450657 0.6035464 0.9931883 0.0722563 0.8549029 0.9826710 -0.5707087 0.2083210 -0.7684904 0.3338464 -0.6956115 0.4054801
Lawsonibacter_asaccharolyticus 1.9588727 0.0000000 0.0000000 -0.8992651 0.0000500 0.0064196 -0.8427373 0.0064474 0.1077099 -0.9557929 0.0020492 0.0831380 -0.1130556 0.7936870 0.9826710 -1.3253889 -0.4731413 -1.4457077 -0.2397669 -1.5580823 -0.3535035
Lawsonibacter_hominis 0.4849402 0.0315789 0.0684610 -0.1495161 0.5047078 0.7827994 -0.0105741 0.9733839 0.9973905 -0.2884581 0.3628030 0.8507175 -0.2778840 0.5352710 0.9826710 -0.5911191 0.2920868 -0.6354478 0.6142996 -0.9126260 0.3357097
Ligaoa_zhengdingensis -0.1258158 0.6140446 0.7295197 0.7117978 0.0048143 0.0911508 0.8179839 0.0215001 0.1795889 0.6056117 0.0871988 0.6432181 -0.2123722 0.6703448 0.9826710 0.2200954 1.2035002 0.1222188 1.5137490 -0.0893675 1.3005909
Mediterraneibacter_faecis -1.4536733 0.0000000 0.0000001 -0.2829388 0.2370095 0.5384855 -1.0963285 0.0014031 0.0498102 0.5304508 0.1173646 0.6732760 1.6267793 0.0008143 0.0770871 -0.7536857 0.1878081 -1.7624412 -0.4302157 -0.1349096 1.1958112
Odoribacter_splanchnicus 0.2648767 0.1859007 0.2916895 -0.1111377 0.5780297 0.8025543 -0.3683311 0.1935738 0.5389703 0.1460557 0.6049840 0.9931883 0.5143868 0.1989213 0.7532486 -0.5048745 0.2825991 -0.9254736 0.1888114 -0.4104575 0.7025689
Oliverpabstia_intestinalis -0.7052688 0.0003081 0.0012867 -0.1007309 0.5990899 0.8025543 -0.5984639 0.0283904 0.1966557 0.3970020 0.1438264 0.6749058 0.9954659 0.0101055 0.2609051 -0.4783600 0.2768981 -1.1328137 -0.0641140 -0.1367443 0.9307483
Oscillibacter_sp_ER4 0.6283839 0.0372485 0.0795381 -0.1308508 0.6624328 0.8325810 -0.2234863 0.5982897 0.8329130 -0.0382153 0.9281038 1.0000000 0.1852710 0.7572418 0.9826710 -0.7216528 0.4599512 -1.0594785 0.6125058 -0.8732632 0.7968326
Oscillibacter_sp_MSJ_31 0.8697484 0.0144744 0.0373703 -0.2125747 0.5465890 0.7844941 0.0310984 0.9502725 0.9973905 -0.4562478 0.3602904 0.8507175 -0.4873461 0.4895938 0.9826710 -0.9073931 0.4822437 -0.9520783 1.0142751 -1.4383139 0.5258184
Oscillibacter_sp_PC13 -0.3972345 0.1112721 0.1858899 -0.2096516 0.3993022 0.7078181 -0.1168502 0.7396606 0.9093663 -0.3024530 0.3896454 0.8782484 -0.1856028 0.7088344 0.9826710 -0.6995379 0.2802348 -0.8100454 0.5763451 -0.9948652 0.3899593
Oscillibacter_valericigenes 1.4061310 0.0000000 0.0000005 -0.2038101 0.4062382 0.7078181 -0.0131446 0.9697716 0.9973905 -0.3944756 0.2558487 0.7568859 -0.3813310 0.4371171 0.9815046 -0.6871361 0.2795159 -0.6970570 0.6707678 -1.0776155 0.2886643
Oscillospiraceae_bacterium 1.2006532 0.0000111 0.0000674 -0.0414810 0.8756886 0.9580197 -0.2455510 0.5130897 0.8070408 0.1625890 0.6644973 0.9931883 0.4081400 0.4419333 0.9815046 -0.5642717 0.4813096 -0.9853063 0.4942043 -0.5763308 0.9015087
Oscillospiraceae_bacterium_CLA_AA_H250 0.8175269 0.0001421 0.0006618 -0.2992005 0.1557009 0.4779906 -0.4916795 0.0995683 0.4022204 -0.1067215 0.7193569 0.9931883 0.3849580 0.3602102 0.9455563 -0.7134392 0.1150382 -1.0778324 0.0944734 -0.6922124 0.4787693
Oscillospiraceae_bacterium_Marseille_Q3528 0.5816455 0.0003307 0.0013610 -0.1022951 0.5197247 0.7830163 -0.3112280 0.1672826 0.5054071 0.1066378 0.6348254 0.9931883 0.4178658 0.1894496 0.7379384 -0.4153930 0.2108028 -0.7542654 0.1318094 -0.3358992 0.5491748
Parabacteroides_distasonis 0.6122706 0.0052642 0.0151013 0.0937553 0.6654785 0.8325810 -0.0658529 0.8300288 0.9582446 0.2533635 0.4087901 0.8873087 0.3192164 0.4619465 0.9815046 -0.3336671 0.5211777 -0.6706609 0.5389552 -0.3507614 0.8574884
Parabacteroides_merdae 0.1022504 0.6455861 0.7576299 0.0343838 0.8770603 0.9580197 0.0278964 0.9293200 0.9973905 0.0408713 0.8964864 1.0000000 0.0129749 0.9767139 0.9948202 -0.4038351 0.4726028 -0.5921889 0.6479816 -0.5785136 0.6602562
Paraprevotella_clara -0.5857004 0.1014457 0.1720178 -0.1364271 0.7017091 0.8589888 -0.2783744 0.5808281 0.8281574 0.0055202 0.9912495 1.0000000 0.2838946 0.6902582 0.9826710 -0.8385634 0.5657092 -1.2719060 0.7151572 -0.9868891 0.9979296
Parasutterella_excrementihominis 0.8118271 0.0056638 0.0154665 0.2259393 0.4362976 0.7255890 0.2803670 0.4947214 0.7983005 0.1715116 0.6756781 0.9931883 -0.1088555 0.8511171 0.9826710 -0.3457793 0.7976578 -0.5286219 1.0893559 -0.6365635 0.9795867
Phascolarctobacterium_faecium -0.1912047 0.4726104 0.6025692 -0.1327721 0.6178152 0.8158003 -0.0820245 0.8275027 0.9582446 -0.1835197 0.6255895 0.9931883 -0.1014952 0.8487066 0.9826710 -0.6572385 0.3916942 -0.8241509 0.6601019 -0.9248079 0.5577685
Phocaeicola_dorei -0.4047226 0.2898138 0.4178027 -0.9672770 0.0120868 0.1252238 -0.3236079 0.5492739 0.8080869 -1.6109461 0.0032177 0.1031732 -1.2873382 0.0931415 0.5878263 -1.7198268 -0.2147272 -1.3884753 0.7412595 -2.6746107 -0.5472815
Phocaeicola_sartorii -1.8490959 0.0000000 0.0000000 0.2294912 0.2491412 0.5571346 0.0000000 1.0000000 1.0000000 0.4589824 0.1036563 0.6690543 0.4589824 0.2491412 0.8073470 -0.1623318 0.6213142 -0.5544344 0.5544344 -0.0948258 1.0127905
Phocaeicola_vulgatus -0.6355390 0.0723552 0.1325734 0.4617757 0.1906478 0.4996872 0.3701501 0.4576813 0.7709511 0.5534014 0.2668141 0.7654060 0.1832513 0.7946109 0.9826710 -0.2321056 1.1556570 -0.6117006 1.3520008 -0.4273403 1.5341431
Phocea_massiliensis -0.0100617 0.9577975 0.9714803 0.0579048 0.7607483 0.8861676 0.1794723 0.5050217 0.8057649 -0.0636628 0.8127571 1.0000000 -0.2431350 0.5228466 0.9826710 -0.3169831 0.4327926 -0.3509987 0.7099433 -0.5935346 0.4662091
Provencibacterium_massiliense -0.2413713 0.2941269 0.4218789 0.6898911 0.0030466 0.0665572 1.0148027 0.0020921 0.0639477 0.3649796 0.2618234 0.7619261 -0.6498231 0.1584590 0.6815147 0.2370368 1.1427455 0.3740081 1.6555972 -0.2750912 1.0050503
Pseudoflavonifractor_capillosus 0.1817008 0.4378126 0.5677569 0.2876177 0.2200256 0.5213278 0.3629458 0.2738353 0.6590613 0.2122897 0.5211640 0.9931883 -0.1506561 0.7475198 0.9826710 -0.1736841 0.7489196 -0.2898021 1.0156937 -0.4397209 0.8643003
Roseburia_faecis -0.3893694 0.1767272 0.2788362 -0.1889794 0.5111342 0.7827994 -0.3272513 0.4214828 0.7400735 -0.0507076 0.9006665 1.0000000 0.2765437 0.6305777 0.9826710 -0.7556691 0.3777103 -1.1291243 0.4746218 -0.8516749 0.7502597
Roseburia_hominis -0.2859875 0.2694934 0.3924929 0.8663516 0.0009833 0.0310291 0.5702630 0.1203781 0.4327516 1.1624402 0.0017285 0.0831380 0.5921773 0.2530066 0.8073470 0.3566663 1.3760369 -0.1509481 1.2914740 0.4420438 1.8828367
Roseburia_intestinalis -0.5229867 0.0741642 0.1350169 0.0327740 0.9104664 0.9605496 0.0164864 0.9681119 0.9973905 0.0490616 0.9051982 1.0000000 0.0325753 0.9554335 0.9948202 -0.5418651 0.6074132 -0.7966352 0.8296080 -0.7631415 0.8612648
Roseburia_inulinivorans -1.0431121 0.0002938 0.0012456 -0.3791003 0.1804782 0.4976292 -0.2064062 0.6054739 0.8388028 -0.5517944 0.1679050 0.6963755 -0.3453882 0.5409108 0.9826710 -0.9356571 0.1774564 -0.9939410 0.5811286 -1.3384396 0.2348508
Ruminococcus_bicirculans -0.1047783 0.6955478 0.8032351 -0.4393053 0.1021796 0.4087186 -0.8579763 0.0246095 0.1839238 -0.0206343 0.9565062 1.0000000 0.8373420 0.1191864 0.6535935 -0.9670832 0.0884726 -1.6047886 -0.1111640 -0.7666031 0.7253344
Ruminococcus_bromii -1.3652069 0.0000019 0.0000133 -0.3373149 0.2233416 0.5213278 -0.5313707 0.1754555 0.5128561 -0.1432592 0.7138742 0.9931883 0.3881115 0.4829241 0.9826710 -0.8822390 0.2076091 -1.3024450 0.2397036 -0.9134625 0.6269442
Ruminococcus_torques -1.1589855 0.0000001 0.0000010 0.1739815 0.4039641 0.7078181 -0.8929241 0.0028037 0.0663551 1.2408871 0.0000402 0.0114147 2.1338112 0.0000008 0.0002314 -0.2366105 0.5845735 -1.4739169 -0.3119313 0.6605506 1.8212237
Ruthenibacterium_lactatiformans 0.8552637 0.0000421 0.0002135 -0.6232332 0.0025233 0.0597181 -0.8921945 0.0022517 0.0639477 -0.3542718 0.2189749 0.7316337 0.5379228 0.1873031 0.7379384 -1.0243234 -0.2221429 -1.4597422 -0.3246468 -0.9211784 0.2126349
Segatella_copri -0.1041270 0.8348932 0.8749434 1.0330103 0.0399354 0.2700392 0.1368109 0.8465393 0.9616687 1.9292096 0.0069016 0.1507742 1.7923987 0.0742296 0.5855892 0.0480735 2.0179470 -1.2568869 1.5305087 0.5370861 3.3213332
Simiaoa_sunii -0.2363296 0.5239407 0.6469529 -0.3579564 0.3348070 0.6696140 -0.6887912 0.1902072 0.5389703 -0.0271216 0.9587069 1.0000000 0.6616696 0.3726144 0.9620225 -1.0886706 0.3727577 -1.7227608 0.3451784 -1.0599233 1.0056801
Streptococcus_salivarius -0.4179784 0.0877112 0.1547204 -0.0171126 0.9440127 0.9749077 0.0061247 0.9858280 0.9973905 -0.0403498 0.9067381 1.0000000 -0.0464745 0.9240278 0.9826710 -0.4975543 0.4633291 -0.6737064 0.6859557 -0.7194130 0.6387133
Streptococcus_thermophilus -0.6572501 0.0003886 0.0015543 -0.0137621 0.9396140 0.9749077 -0.3507073 0.1736996 0.5128561 0.3231831 0.2092628 0.7316337 0.6738903 0.0650362 0.5597053 -0.3719441 0.3444199 -0.8575392 0.1561247 -0.1830764 0.8294426
Sutterella_wadsworthensis 1.4557556 0.0001249 0.0006012 0.5439886 0.1437487 0.4692485 0.2625218 0.6170311 0.8465547 0.8254554 0.1167046 0.6732760 0.5629336 0.4482851 0.9815046 -0.1872299 1.2752071 -0.7721615 1.2972051 -0.2080592 1.8589700
Vescimonas_coprocola 1.3129706 0.0000000 0.0000002 -0.3893766 0.0785517 0.3718112 -0.6790551 0.0305588 0.2066360 -0.0996981 0.7488483 0.9931883 0.5793570 0.1896814 0.7379384 -0.8237049 0.0449517 -1.2936350 -0.0644751 -0.7135839 0.5141877
Wansuia_hejianensis -1.1041237 0.0004405 0.0017135 0.1375377 0.6554774 0.8325810 0.4232449 0.3324511 0.6856880 -0.1481694 0.7337735 0.9931883 -0.5714143 0.3545101 0.9442582 -0.4700739 0.7451494 -0.4365332 1.2830230 -1.0069764 0.7106375
Youxingia_wuxianensis -0.4377250 0.1017570 0.1720178 0.6868936 0.0106918 0.1167873 1.1477132 0.0026781 0.0663551 0.2260740 0.5484359 0.9931883 -0.9216392 0.0850760 0.5878263 0.1616680 1.2121191 0.4045125 1.8909139 -0.5162872 0.9684352
bacterium_210917_DFI_7_65 0.3618194 0.0314552 0.0684610 -0.2681676 0.1096934 0.4222573 -0.1721624 0.4666036 0.7735065 -0.3641727 0.1242124 0.6749058 -0.1920103 0.5655384 0.9826710 -0.5974095 0.0610743 -0.6380438 0.2937190 -0.8295279 0.1011825
Bacteroides_faecis 0.0789161 0.7127340 0.8129174 -0.0093742 0.9651077 0.9832997 0.1221415 0.6871648 0.8835689 -0.1408899 0.6419269 0.9931883 -0.2630314 0.5396354 0.9826710 -0.4318877 0.4131393 -0.4757204 0.7200034 -0.7380765 0.4562967
Clostridiaceae_unclassified_SGB4771 0.4615174 0.0136171 0.0354795 0.1625183 0.3810267 0.7078181 0.2687619 0.3061427 0.6856880 0.0562748 0.8298847 1.0000000 -0.2124871 0.5666020 0.9826710 -0.2028356 0.5278722 -0.2482185 0.7857422 -0.4601216 0.5726712
Clostridium_sp_AM49_4BH -0.4396135 0.0383255 0.0810006 0.0726905 0.7303024 0.8751303 0.1737274 0.5605392 0.8080869 -0.0283465 0.9242152 1.0000000 -0.2020739 0.6318888 0.9826710 -0.3429916 0.4883725 -0.4144679 0.7619227 -0.6158774 0.5591845
Colidextribacter_sp_210702_DFI_3_9 0.1991055 0.2176704 0.3270814 -0.0957784 0.5524607 0.7844941 -0.0560480 0.8058414 0.9471457 -0.1355087 0.5520673 0.9931883 -0.0794606 0.8052615 0.9826710 -0.4134818 0.2219251 -0.5056024 0.3935063 -0.5845552 0.3135379
Enterocloster_lavalensis -0.4474452 0.0870625 0.1545359 -0.3699728 0.1565251 0.4779906 -0.2230924 0.5449670 0.8080869 -0.5168533 0.1613622 0.6963755 -0.2937608 0.5727743 0.9826710 -0.8832221 0.1432764 -0.9493465 0.5031616 -1.2422870 0.2085805
GGB2982_SGB3964 -0.8860770 0.0000000 0.0000004 -0.2014363 0.1913554 0.4996872 -0.2550869 0.2420356 0.6192621 -0.1477856 0.4968118 0.9892978 0.1073012 0.7272015 0.9826710 -0.5046075 0.1017350 -0.6840779 0.1739042 -0.5762921 0.2807209
GGB3304_SGB4367 -0.0673165 0.8493379 0.8868087 0.0101433 0.9771634 0.9840937 -0.4883264 0.3308050 0.6856880 0.5086129 0.3106256 0.8019788 0.9969393 0.1607799 0.6815147 -0.6885100 0.7087965 -1.4769295 0.5002767 -0.4788736 1.4960994
GGB3619_SGB4894 -0.2683504 0.1467404 0.2371081 -0.0177214 0.9234074 0.9677037 0.0249808 0.9236973 0.9973905 -0.0604235 0.8166058 1.0000000 -0.0854043 0.8168076 0.9826710 -0.3811426 0.3456998 -0.4892647 0.5392263 -0.5740882 0.4532411
GGB9296_SGB14253 0.3806099 0.0155446 0.0397718 0.1003910 0.5198547 0.7830163 -0.2000293 0.3651202 0.6934416 0.4008112 0.0703175 0.6187951 0.6008406 0.0553420 0.5300197 -0.2069746 0.4077565 -0.6349555 0.2348968 -0.0336236 0.8352461
GGB9524_SGB14924 -0.0119401 0.9499163 0.9669399 -0.2520040 0.1861311 0.4996872 -0.0207228 0.9385911 0.9973905 -0.4832852 0.0734797 0.6187951 -0.4625624 0.2247831 0.7792030 -0.6268029 0.1227949 -0.5510679 0.5096223 -1.0130313 0.0464609
GGB9574_SGB14987 -0.4419731 0.0394968 0.0824787 -0.3269348 0.1266194 0.4494990 -0.1542460 0.6093783 0.8401138 -0.4996236 0.0988141 0.6526324 -0.3453776 0.4185308 0.9815046 -0.7473949 0.0935253 -0.7492022 0.4407102 -1.0939078 0.0946606
GGB9619_SGB15066 -0.4246423 0.0239306 0.0552544 -0.3185963 0.0891093 0.3878452 0.1406080 0.5944457 0.8329130 -0.7778005 0.0036012 0.1031732 -0.9184085 0.0147353 0.3219095 -0.6864301 0.0492376 -0.3798815 0.6610975 -1.2977021 -0.2578989
GGB9707_SGB15229 0.7627442 0.0000137 0.0000793 0.3176839 0.0634975 0.3339497 0.2351989 0.3297158 0.6856880 0.4001689 0.0978007 0.6526324 0.1649700 0.6282270 0.9826710 -0.0180582 0.6534260 -0.2398803 0.7102781 -0.0743737 0.8747115
GGB9708_SGB15233 -0.0800176 0.7569525 0.8431227 0.6390531 0.0143199 0.1355621 0.3570830 0.3296891 0.6856880 0.9210233 0.0125451 0.2375212 0.5639404 0.2762677 0.8436038 0.1293520 1.1487543 -0.3641505 1.0783164 0.2006045 1.6414421
GGB9760_SGB15374 -0.0583757 0.7862139 0.8587875 -0.5798821 0.0076977 0.1151234 -0.6279265 0.0404917 0.2446731 -0.5318378 0.0818042 0.6333906 0.0960888 0.8233516 0.9826710 -1.0041877 -0.1555766 -1.2283242 -0.0275288 -1.1315573 0.0678818
Roseburia_sp_AF02_12 -0.0265258 0.9187149 0.9453443 0.3951687 0.1297825 0.4550398 0.8700957 0.0189943 0.1795889 -0.0797583 0.8281391 1.0000000 -0.9498541 0.0690824 0.5770416 -0.1173052 0.9076426 0.1449388 1.5952527 -0.8040962 0.6445795
Segatella_brunsvicensis -0.1893936 0.5455330 0.6649415 -0.6067839 0.0540313 0.3264869 -0.3215060 0.4684617 0.7735065 -0.8920618 0.0451791 0.4850025 -0.5705558 0.3629072 0.9455563 -1.2242047 0.0106370 -1.1951642 0.5521523 -1.7647332 -0.0193904
Wujia_chipingensis -0.3541156 0.2528818 0.3737999 -0.3409640 0.2708639 0.5827678 -0.5048523 0.2493397 0.6211620 -0.1770757 0.6853076 0.9931883 0.3277766 0.5961061 0.9826710 -0.9503757 0.2684477 -1.3671774 0.3574728 -1.0384268 0.6842754
Alistipes_dispar 0.4417497 0.0115357 0.0306181 0.0463551 0.7889463 0.8998423 0.0694649 0.7768118 0.9287518 0.0232453 0.9243321 1.0000000 -0.0462197 0.8938298 0.9826710 -0.2950493 0.3877594 -0.4136265 0.5525564 -0.4593005 0.5057910
Alistipes_sp_AF17_16 0.3054584 0.0666218 0.1269839 -0.0681526 0.6808713 0.8425971 -0.5632969 0.0172252 0.1687600 0.4269917 0.0696389 0.6187951 0.9902886 0.0031914 0.1510606 -0.3947940 0.2584888 -1.0254986 -0.1010952 -0.0346879 0.8886713
Anaerobutyricum_soehngenii 0.3472927 0.1237902 0.2055930 0.3300713 0.1433974 0.4692485 0.6018775 0.0598961 0.3092817 0.0582650 0.8545275 1.0000000 -0.5436125 0.2277248 0.7792030 -0.1132123 0.7733548 -0.0253742 1.2291293 -0.5682782 0.6848082
Anaerosacchariphilus_sp_NSJ_68 0.4661447 0.0824459 0.1475889 -0.0816167 0.7600224 0.8861676 0.2315507 0.5404370 0.8080869 -0.3947841 0.2966156 0.7947059 -0.6263348 0.2421135 0.7995375 -0.6083719 0.4451384 -0.5138145 0.9769158 -1.1393073 0.3497391
Anaerotignum_sp_MSJ_24 0.1388950 0.4129350 0.5429330 -0.1980172 0.2436144 0.5490991 -0.2746018 0.2531165 0.6250878 -0.1214325 0.6123227 0.9931883 0.1531693 0.6514369 0.9826710 -0.5321541 0.1361197 -0.7474097 0.1982061 -0.5937064 0.3508413
Bittarella_massiliensis -0.7916882 0.0001665 0.0007505 0.1749451 0.3955252 0.7078181 0.5910586 0.0435791 0.2500470 -0.2411683 0.4072631 0.8873087 -0.8322270 0.0443762 0.5300197 -0.2305783 0.5804686 0.0172378 1.1648794 -0.8143410 0.3320043
Blautia_SGB4815 -0.0629407 0.7987501 0.8658207 -0.3001179 0.2250930 0.5213278 -0.3355400 0.3374033 0.6856880 -0.2646958 0.4484352 0.9364381 0.0708442 0.8858949 0.9826710 -0.7867956 0.1865598 -1.0241950 0.3531150 -0.9525730 0.4231814
Blautia_luti 0.0349915 0.8842407 0.9198694 -0.3145323 0.1917813 0.4996872 -0.1555712 0.6474347 0.8673181 -0.4734933 0.1645963 0.6963755 -0.3179221 0.5086164 0.9826710 -0.7883750 0.1593105 -0.8260646 0.5149221 -1.1432293 0.1962427
Blautia_sp_OF03_15BH 0.1564994 0.4731441 0.6025692 0.1366827 0.5308861 0.7830163 -0.0129322 0.9665572 0.9973905 0.2862976 0.3534081 0.8507175 0.2992299 0.4928000 0.9826710 -0.2931073 0.5664727 -0.6210904 0.5952259 -0.3211736 0.8937689
Butyricimonas_paravirosa 0.2950980 0.0801592 0.1450013 0.3161937 0.0609933 0.3339497 0.1609817 0.4982153 0.7993964 0.4714057 0.0482653 0.4895481 0.3104240 0.3557593 0.9442582 -0.0147552 0.6471425 -0.3073151 0.6292784 0.0036379 0.9391734
Catenibacillus_scindens -0.5340728 0.0198504 0.0486526 0.1458395 0.5215268 0.7830163 0.1835638 0.5685102 0.8154389 0.1081152 0.7366043 0.9931883 -0.0754486 0.8682323 0.9826710 -0.3024717 0.5941506 -0.4508021 0.8179296 -0.5255341 0.7417644
Clostridiaceae_bacterium_Marseille_Q4149 0.1807571 0.4714150 0.6025692 -0.6713435 0.0080981 0.1151234 -0.5308988 0.1359868 0.4597647 -0.8117882 0.0230925 0.3279139 -0.2808894 0.5756552 0.9826710 -1.1658147 -0.1768723 -1.2305817 0.1687841 -1.5106807 -0.1128956
Clostridium_SGB6173 0.0403818 0.8284416 0.8746372 0.2556415 0.1713190 0.4901612 0.6779040 0.0109170 0.1409286 -0.1666210 0.5272146 0.9931883 -0.8445250 0.0245475 0.3873056 -0.1117491 0.6230320 0.1580418 1.1977662 -0.6858960 0.3526540
Clostridium_SGB6179 0.1688982 0.3854633 0.5237874 0.1073700 0.5808815 0.8025543 0.4356940 0.1145848 0.4279945 -0.2209541 0.4217385 0.8926598 -0.6566480 0.0926353 0.5878263 -0.2758927 0.4906326 -0.1066275 0.9780154 -0.7626629 0.3207548
Clostridium_sp_Marseille_P3244 0.2250229 0.3807563 0.5198789 0.3844349 0.1351631 0.4665397 0.5700606 0.1175478 0.4279945 0.1988093 0.5834944 0.9931883 -0.3712513 0.4694842 0.9826710 -0.1211465 0.8900164 -0.1453434 1.2854646 -0.5157866 0.9134053
Clostridium_sp_NSJ_42 0.2600848 0.1469402 0.2371081 0.2764447 0.1233140 0.4487171 0.6316061 0.0133702 0.1650927 -0.0787167 0.7553827 0.9931883 -0.7103228 0.0482540 0.5300197 -0.0759580 0.6288473 0.1329519 1.1302602 -0.5768076 0.4193742
Coprobacter_secundus -0.3775626 0.0533082 0.1058709 0.0948710 0.6254073 0.8165266 0.1618368 0.5562300 0.8080869 0.0279052 0.9190482 1.0000000 -0.1339317 0.7303452 0.9826710 -0.2881379 0.4778799 -0.3801256 0.7037992 -0.5134450 0.5692554
Eubacteriaceae_bacterium -0.5982870 0.0325065 0.0699382 0.0627743 0.8212655 0.9218949 0.1499005 0.7030581 0.8924991 -0.0243520 0.9505545 1.0000000 -0.1742524 0.7538745 0.9826710 -0.4850378 0.6105864 -0.6252605 0.9250614 -0.7986374 0.7499334
Faecalibacillus_faecis -0.0435143 0.8219887 0.8743250 -0.0886230 0.6468761 0.8286728 -0.0617467 0.8214959 0.9582446 -0.1154992 0.6727141 0.9931883 -0.0537525 0.8894749 0.9826710 -0.4699289 0.2926829 -0.6012993 0.4778059 -0.6544424 0.4234439
Faecalibacillus_intestinalis -1.7170453 0.0000000 0.0000000 -0.3112619 0.1632817 0.4843937 -0.7352125 0.0206211 0.1795889 0.1126886 0.7202678 0.9931883 0.8479011 0.0582242 0.5334086 -0.7501495 0.1276257 -1.3562439 -0.1141810 -0.5076414 0.7330186
GGB13489_SGB15224 0.6984899 0.0000061 0.0000388 -0.0945234 0.5278201 0.7830163 -0.2061910 0.3308308 0.6856880 0.0171442 0.9353903 1.0000000 0.2233353 0.4558702 0.9815046 -0.3895387 0.2004919 -0.6236414 0.2112593 -0.3998346 0.4341230
GGB2970_SGB3952 -0.4794550 0.0000320 0.0001682 -0.2280363 0.0434524 0.2804653 -0.2305924 0.1477506 0.4662351 -0.2254802 0.1564177 0.6950289 0.0051121 0.9818270 0.9948202 -0.4492868 -0.0067858 -0.5436646 0.0824798 -0.5381988 0.0872384
GGB3352_SGB4436 0.0422840 0.8320377 0.8749434 0.0288764 0.8848337 0.9582003 -0.0280124 0.9208988 0.9973905 0.0857653 0.7608724 0.9943154 0.1137778 0.7753925 0.9826710 -0.3641865 0.4219394 -0.5842014 0.5281765 -0.4697954 0.6413260
GGB34797_SGB14322 -0.2328707 0.0946398 0.1628951 -0.1937687 0.1637387 0.4843937 -0.3925484 0.0468593 0.2510951 0.0050110 0.9796111 1.0000000 0.3975594 0.1531777 0.6692687 -0.4672862 0.0797488 -0.7795791 -0.0055177 -0.3815826 0.3916045
GGB34900_SGB14891 -0.4017370 0.0714289 0.1325734 0.3865246 0.0827192 0.3851189 0.4782671 0.1287807 0.4460210 0.2947822 0.3475620 0.8507175 -0.1834849 0.6791296 0.9826710 -0.0506505 0.8236998 -0.1403412 1.0968754 -0.3231274 0.9126917
GGB3653_SGB4964 -0.6468103 0.0016089 0.0051571 -0.1207795 0.5499355 0.7844941 -0.0096144 0.9731551 0.9973905 -0.2319446 0.4168347 0.8926598 -0.2223302 0.5821052 0.9826710 -0.5188776 0.2773186 -0.5729282 0.5536994 -0.7946221 0.3307330
GGB4456_SGB6141 0.8210081 0.0000018 0.0000133 0.2439652 0.1431954 0.4692485 0.5715070 0.0159565 0.1687600 -0.0835766 0.7218815 0.9931883 -0.6550835 0.0499554 0.5300197 -0.0835120 0.5714424 0.1081227 1.0348912 -0.5464375 0.3792843
GGB4552_SGB6276 -1.0711535 0.0000014 0.0000103 -0.3602986 0.0934772 0.3904046 -0.1280490 0.6722914 0.8835689 -0.5925482 0.0513297 0.5026774 -0.4644993 0.2783803 0.8436038 -0.7819797 0.0613825 -0.7247330 0.4686351 -1.1885584 0.0034619
GGB51441_SGB71759 0.4990769 0.0189686 0.0476732 -0.0639488 0.7617701 0.8861676 -0.0868041 0.7711910 0.9280434 -0.0410935 0.8903636 1.0000000 0.0457106 0.9137087 0.9826710 -0.4797994 0.3519018 -0.6752379 0.5016297 -0.6288626 0.5466756
GGB58158_SGB79798 -0.5324471 0.0661131 0.1269839 0.5180488 0.0737022 0.3672179 0.9886311 0.0162879 0.1687600 0.0474664 0.9072472 1.0000000 -0.9411647 0.1039520 0.6150495 -0.0502459 1.0863434 0.1844871 1.7927752 -0.7557693 0.8507022
GGB9365_SGB14341 0.1584319 0.3889591 0.5260209 0.1681830 0.3605081 0.6964919 0.0126137 0.9612953 0.9973905 0.3237524 0.2135024 0.7316337 0.3111387 0.3975663 0.9815046 -0.1939929 0.5303589 -0.4998697 0.5250970 -0.1881522 0.8356569
GGB9412_SGB14770 -0.0512085 0.7716316 0.8526980 0.2391891 0.1763663 0.4910590 0.1737368 0.4867589 0.7899402 0.3046414 0.2228544 0.7359378 0.1309046 0.7106806 0.9826710 -0.1086357 0.5870139 -0.3184396 0.6659132 -0.1869791 0.7962619
GGB9627_SGB15081 -0.5570538 0.0007363 0.0025193 0.0950715 0.5577933 0.7881259 0.0977297 0.6701766 0.8835689 0.0924132 0.6867985 0.9931883 -0.0053165 0.9869177 0.9948202 -0.2245717 0.4147147 -0.3545694 0.5500289 -0.3593750 0.5442015
GGB9712_SGB15244 0.0834814 0.6647895 0.7737714 -0.2371537 0.2192856 0.5213278 -0.3347496 0.2204167 0.5796144 -0.1395578 0.6083426 0.9931883 0.1951917 0.6124936 0.9826710 -0.6169049 0.1425975 -0.8721023 0.2026031 -0.6763036 0.3971879
GGB9747_SGB15356 -0.1490394 0.5996523 0.7155514 -0.3152190 0.2676331 0.5802121 -0.4648212 0.2480818 0.6211620 -0.1656168 0.6797936 0.9931883 0.2992044 0.5982761 0.9826710 -0.8748132 0.2443752 -1.2566540 0.3270115 -0.9565551 0.6253216
GGB9767_SGB15385 -0.0062842 0.9679194 0.9782531 -0.0856220 0.5838894 0.8025543 -0.4515128 0.0424467 0.2500470 0.2802689 0.2055515 0.7316337 0.7317818 0.0202257 0.3378885 -0.3937033 0.2224594 -0.8874518 -0.0155739 -0.1551776 0.7157154
GGB9787_SGB15410 0.2360569 0.2057461 0.3193000 0.3526064 0.0595125 0.3339497 0.3565285 0.1769715 0.5128561 0.3486844 0.1861412 0.7241659 -0.0078441 0.9831853 0.9948202 -0.0143073 0.7195201 -0.1626590 0.8757159 -0.1699166 0.8672854
GGB9790_SGB15413 0.3371675 0.0211895 0.0497341 0.1365694 0.3472641 0.6848819 0.2538239 0.2174562 0.5771735 0.0193148 0.9249691 1.0000000 -0.2345091 0.4195116 0.9815046 -0.1495240 0.4226627 -0.1510018 0.6586496 -0.3850536 0.4236833
Haemophilus_parainfluenzae 0.0638538 0.7535948 0.8431227 0.4207131 0.0398767 0.2700392 0.3354792 0.2447313 0.6205685 0.5059470 0.0798354 0.6333906 0.1704678 0.6752478 0.9826710 0.0196989 0.8217273 -0.2319609 0.9029193 -0.0608521 1.0727462
Intestinibacter_bartlettii 0.5145710 0.0076595 0.0205216 -0.1620575 0.3963093 0.7078181 -0.4471369 0.0991797 0.4022204 0.1230218 0.6484378 0.9931883 0.5701587 0.1365697 0.6639826 -0.5383330 0.2142179 -0.9795713 0.0852975 -0.4088112 0.6548548
Lachnospira_sp_NSJ_43 -0.7003931 0.0015555 0.0050777 0.3853736 0.0784363 0.3718112 1.1318870 0.0003217 0.0152257 -0.3611398 0.2420300 0.7493886 -1.4930268 0.0007639 0.0770871 -0.0443219 0.8150692 0.5238625 1.7399116 -0.9684775 0.2461980
Lachnospiraceae_bacterium_OM04_12BH -0.1982599 0.4356230 0.5675089 -0.1221019 0.6309328 0.8165266 -0.2357325 0.5122950 0.8070408 -0.0084713 0.9811796 1.0000000 0.2272611 0.6547992 0.9826710 -0.6230419 0.3788381 -0.9445688 0.4731039 -0.7165070 0.6995644
Lactococcus_lactis 0.4473450 0.0003578 0.0014516 0.3209600 0.0097287 0.1151234 0.6419199 0.0002972 0.0152257 0.0000000 1.0000000 1.0000000 -0.6419199 0.0097287 0.2609051 0.0787101 0.5632099 0.2991333 0.9847065 -0.3423994 0.3423994
Lentihominibacter_faecis -0.0313566 0.8998784 0.9293289 -0.2603615 0.2969755 0.6247484 -0.3249500 0.3574471 0.6934416 -0.1957731 0.5785471 0.9931883 0.1291770 0.7955319 0.9826710 -0.7517445 0.2310214 -1.0202630 0.3703630 -0.8903007 0.4987546
Massilioclostridium_coli 0.4530499 0.0587710 0.1151100 0.3410670 0.1538211 0.4779906 0.3193175 0.3445170 0.6904493 0.3628164 0.2824522 0.7788002 0.0434989 0.9273093 0.9826710 -0.1289750 0.8111089 -0.3457977 0.9844327 -0.3015475 1.0271804
Mediterraneibacter_butyricigenes 0.7943287 0.0036954 0.0112850 -0.6048010 0.0262544 0.2130359 -0.6006765 0.1173645 0.4279945 -0.6089256 0.1120486 0.6732760 -0.0082492 0.9878144 0.9948202 -1.1372673 -0.0723348 -1.3541228 0.1527699 -1.3615210 0.1436697
Mediterraneibacter_sp_NSJ_151 0.2955616 0.0527045 0.1054091 0.0802774 0.5967777 0.8025543 0.1389126 0.5177483 0.8079149 0.0216422 0.9195899 1.0000000 -0.1172705 0.6991316 0.9826710 -0.2187776 0.3793324 -0.2842539 0.5620792 -0.4010464 0.4443307
Methanobrevibacter_smithii -0.7057619 0.0004010 0.0015819 -0.1525634 0.4357187 0.7255890 -0.3434011 0.2156819 0.5771735 0.0382742 0.8898662 1.0000000 0.3816754 0.3298237 0.9442582 -0.5381235 0.2329966 -0.8889735 0.2021712 -0.5066819 0.5832303
Romboutsia_timonensis -0.0999055 0.6404656 0.7547395 0.2088686 0.3293957 0.6634636 0.0206706 0.9455358 0.9973905 0.3970667 0.1901073 0.7296010 0.3763960 0.3793734 0.9699910 -0.2127460 0.6304833 -0.5759194 0.6172607 -0.1988495 0.9929828
Ruminococcus_gnavus 0.2341570 0.3938601 0.5301245 0.0712007 0.7952275 0.9001083 -0.3390500 0.3829657 0.7153866 0.4814514 0.2154238 0.7316337 0.8205014 0.1361205 0.6639826 -0.4696635 0.6120649 -1.1043796 0.4262795 -0.2830137 1.2459165
Ruminococcus_lactaris -0.8025082 0.0000045 0.0000297 -0.4443154 0.0093995 0.1151234 -0.5387120 0.0256473 0.1867649 -0.3499189 0.1449622 0.6749058 0.1887931 0.5773089 0.9826710 -0.7781084 -0.1105225 -1.0110331 -0.0663908 -0.8217066 0.1218688
Ruminococcus_sp_AF41_9 -0.1280947 0.4991576 0.6297176 0.3543767 0.0627493 0.3339497 0.3717707 0.1666549 0.5054071 0.3369827 0.2092291 0.7316337 -0.0347881 0.9268307 0.9826710 -0.0190715 0.7278249 -0.1566632 0.9002046 -0.1908544 0.8648197
Senegalimassilia_anaerobia -0.1985857 0.1656382 0.2642768 0.0764502 0.5926054 0.8025543 0.0898192 0.6568114 0.8716562 0.0630813 0.7546960 0.9931883 -0.0267379 0.9254210 0.9826710 -0.2051382 0.3580387 -0.3086320 0.4882703 -0.3349198 0.4610824
Slackia_isoflavoniconvertens -0.0910798 0.4436485 0.5727098 0.0524237 0.6590762 0.8325810 0.0213488 0.8989345 0.9973905 0.0834987 0.6190959 0.9931883 0.0621499 0.7936509 0.9826710 -0.1817870 0.2866345 -0.3100623 0.3527599 -0.2475381 0.4145355
Streptococcus_parasanguinis 0.1374812 0.5864509 0.7027513 0.2168057 0.3912926 0.7078181 0.0096241 0.9785201 0.9973905 0.4239873 0.2360555 0.7493886 0.4143632 0.4126145 0.9815046 -0.2812646 0.7148761 -0.6951517 0.7143999 -0.2799924 1.1279671
Veillonella_dispar 0.1396031 0.5349718 0.6548793 -0.0265190 0.9061267 0.9605496 -0.0778011 0.8068584 0.9471457 0.0247631 0.9379000 1.0000000 0.1025642 0.8196236 0.9826710 -0.4698978 0.4168598 -0.7051876 0.5495854 -0.6019148 0.6514409
Victivallis_lenta 0.7478215 0.0000044 0.0000297 0.1925994 0.2229544 0.5213278 0.1849707 0.4075675 0.7234323 0.2002280 0.3695361 0.8507175 0.0152573 0.9614111 0.9948202 -0.1182788 0.5034775 -0.2549258 0.6248672 -0.2391716 0.6396277
Bifidobacterium_pseudocatenulatum 0.1203507 0.4836447 0.6131924 0.2342821 0.1736172 0.4901612 0.2016485 0.4070202 0.7234323 0.2669156 0.2722580 0.7655571 0.0652670 0.8492591 0.9826710 -0.1042303 0.5727945 -0.2773507 0.6806478 -0.2115427 0.7453738
Eubacterium_sp_AF34_35BH -0.1732120 0.2540260 0.3737999 -0.1079117 0.4767816 0.7564579 -0.0853573 0.6906771 0.8835689 -0.1304661 0.5427090 0.9931883 -0.0451088 0.8816972 0.9826710 -0.4067214 0.1908981 -0.5081768 0.3374622 -0.5528080 0.2918759
Faecalicatena_contorta 0.7436050 0.0010501 0.0035085 -0.0042480 0.9848137 0.9882937 0.0226852 0.9427334 0.9973905 -0.0311811 0.9212582 1.0000000 -0.0538663 0.9039448 0.9826710 -0.4442737 0.4357777 -0.5999567 0.6453271 -0.6531197 0.5907575
GGB9559_SGB14969 0.4288588 0.0469308 0.0952025 -0.1147603 0.5928451 0.8025543 0.0447283 0.8828604 0.9871353 -0.2742489 0.3663447 0.8507175 -0.3189773 0.4575904 0.9815046 -0.5377301 0.3082095 -0.5537793 0.6432359 -0.8720805 0.3235826
GGB9759_SGB15370 0.1400843 0.3635074 0.4987252 -0.1957374 0.2047352 0.5145558 -0.2151215 0.3241553 0.6856880 -0.1763534 0.4181804 0.8926598 0.0387681 0.8998123 0.9826710 -0.4992994 0.1078245 -0.6446654 0.2144225 -0.6054122 0.2527054
Roseburia_lenta -0.4938826 0.0005303 0.0019559 0.5609384 0.0000904 0.0064196 1.0095993 0.0000009 0.0002573 0.1122776 0.5703443 0.9931883 -0.8973217 0.0015900 0.1128877 0.2851084 0.8367685 0.6192963 1.3999023 -0.2775846 0.5021397
Enterocloster_bolteae -0.2540947 0.3145033 0.4465947 -0.2188847 0.3860567 0.7078181 -0.4251623 0.2345836 0.6056523 -0.0126071 0.9717902 1.0000000 0.4125552 0.4139444 0.9815046 -0.7161986 0.2784292 -1.1288677 0.2785431 -0.7155177 0.6903034
GGB2848_SGB3813 -0.0701420 0.7780317 0.8539447 0.2056502 0.4089785 0.7078181 0.8183528 0.0211441 0.1795889 -0.4070523 0.2480371 0.7493886 -1.2254051 0.0146885 0.3219095 -0.2849040 0.6962044 0.1242125 1.5124931 -1.1004086 0.2863040
GGB3005_SGB3996 -0.2416299 0.3228164 0.4516249 0.3248668 0.1842923 0.4996872 0.5071605 0.1432236 0.4616646 0.1425730 0.6794197 0.9931883 -0.3645876 0.4554351 0.9815046 -0.1562707 0.8060042 -0.1736549 1.1879760 -0.5374735 0.8226195
GGB3061_SGB4063 -0.3720429 0.0205384 0.0489740 0.0578505 0.7165169 0.8659182 0.2082176 0.3562149 0.6934416 -0.0925166 0.6811945 0.9931883 -0.3007342 0.3458221 0.9442582 -0.2562041 0.3719051 -0.2361736 0.6526088 -0.5364058 0.3513726
GGB36331_SGB15121 -0.1610729 0.2037593 0.3179541 -0.1722296 0.1743179 0.4901612 -0.3702019 0.0397876 0.2446731 0.0257426 0.8854516 1.0000000 0.3959445 0.1187410 0.6535935 -0.4214907 0.0770314 -0.7229094 -0.0174944 -0.3265665 0.3780517
Hungatella_hathewayi 0.3805706 0.1354893 0.2224218 0.0637994 0.8017398 0.9035480 0.1111378 0.7572433 0.9190474 0.0164610 0.9634372 1.0000000 -0.0946767 0.8521951 0.9826710 -0.4371209 0.5647197 -0.5976708 0.8199463 -0.6915469 0.7244689
TM7_phylum_sp_oral_taxon_352 0.2211431 0.3533003 0.4870742 0.5046715 0.0351570 0.2560152 0.5483149 0.1048039 0.4022204 0.4610281 0.1716418 0.6963755 -0.0872868 0.8544685 0.9826710 0.0355516 0.9737914 -0.1154956 1.2121254 -0.2020326 1.1240888
Veillonella_parvula 0.4135441 0.0921216 0.1605064 0.5392612 0.0285481 0.2252126 0.6173761 0.0757108 0.3468043 0.4611464 0.1831797 0.7225423 -0.1562297 0.7493454 0.9826710 0.0572857 1.0212368 -0.0646253 1.2993775 -0.2200847 1.1423775
GGB6649_SGB9391 0.1669050 0.2297361 0.3433950 0.0923399 0.5057295 0.7827994 -0.1074148 0.5842290 0.8281574 0.2920945 0.1374522 0.6749058 0.3995093 0.1509900 0.6692687 -0.1810464 0.3657261 -0.4942597 0.2794301 -0.0943134 0.6785025
Veillonella_atypica 0.2057969 0.3028862 0.4322597 0.1782601 0.3719781 0.7078181 0.2997149 0.2890230 0.6783679 0.0568054 0.8402928 1.0000000 -0.2429095 0.5427369 0.9826710 -0.2149378 0.5714580 -0.2566651 0.8560948 -0.4989461 0.6125569
Open code

if(file.exists('gitignore/result_microbiome.csv') == FALSE){
  write.table(result_microbiome, 'gitignore/result_microbiome.csv', row.names = FALSE)
  }

5 Elastic net

To assess the predictive power of microbiome features to discriminate between diet strategy, we employed Elastic Net logistic regression.

As we expected very high level of co-linearity, we allowed \(alpha\) to rather small (0, 0.2 or 0.4). All features were standardized by 2 standard deviations.

The performance of the predictive models was evaluated through their capacity of discriminate between vegan and omnivore diets, using out-of-sample area under ROC curve (AUC; estimated with out-of-bag bootstrap) as the measure of discriminatory capacity.

All features were transformed by 2 standard deviations (resulting in standard deviation of 0.5).

5.1 Prepare data for glmnet

Open code
data_microbiome_glmnet <- data_microbiome_original %>%
  na.omit() %>%
  dplyr::mutate(
    vegan = as.numeric(
      dplyr::if_else(
        Diet == "VEGAN", 1, 0
      )
    ),
    dplyr::across(
      `Adlercreutzia_equolifaciens`:`Veillonella_atypica`, ~ arm::rescale(.)
    )
  ) %>%
  dplyr::select(
    vegan,
    dplyr::everything()
  ) %>%
  dplyr::select(
    Sample, vegan, `Adlercreutzia_equolifaciens`:`Veillonella_atypica`
  )

5.2 Fit model

Open code
modelac <- "elanet_microbiome_all"

assign(
  modelac,
  run(
    expr = clust_glmnet(
      data = data_microbiome_glmnet,
      outcome = "vegan",
      clust_id = "Sample",
      sample_method = "oos_boot",
      N = 500,
      alphas = c(0, 0.2, 0.4),
      family = "binomial",
      seed = 478
    ),
    path = paste0("gitignore/run/", modelac)
  )
)

5.3 Model summary

Open code
elanet_microbiome_all$model_summary
##   alpha     lambda       auc auc_OutOfSample auc_oos_CIL auc_oos_CIU  accuracy
## 1   0.4 0.05671541 0.9867025       0.8202338   0.7314971   0.9017181 0.9216867
##   accuracy_OutOfSample accuracy_oos_CIL accuracy_oos_CIU
## 1            0.7374451        0.6349206        0.8319915

5.4 Calibration plot

Open code
elanet_microbiome_all$plot

Calibration plot, showing outcomes value (y-axis) according to prediction of elastic net model (x-axis). Grey curves show predictions from different bootstrap iterations. Red lines and shadows show average prediction across all iterations and its 95% confidence

5.5 Estimated coefficients

Open code
data.frame(
  microbiome = row.names(
    elanet_microbiome_all$betas
    )[
      which(
        abs(
          elanet_microbiome_all$betas
          )>0
        )
      ],
  beta = elanet_microbiome_all$betas[
    abs(
      elanet_microbiome_all$betas
      )>0
    ]
  ) %>% 
  mutate(
    is_in_ExtValCoh = if_else(
      microbiome %in% names(data_microbiome_validation),
      1, 0
      )
    )
##                                  microbiome         beta is_in_ExtValCoh
## 1                               (Intercept)  0.407222882               0
## 2           Agathobaculum_butyriciproducens  0.621419023               1
## 3                       Anaerofilum_hominis  0.084631010               1
## 4                    Anaerotignum_faecicola -0.193830429               1
## 5                 Anaerotruncus_colihominis  0.093112698               1
## 6                        Bacteroides_ovatus  0.024651413               1
## 7              Barnesiella_intestinihominis -0.095395373               1
## 8                Brotolimicola_acetigignens  0.054915462               1
## 9            Clostridia_bacterium_UC5_1_1D1  0.082518832               1
## 10                       Clostridium_fessum -0.417582156               1
## 11                  Collinsella_aerofaciens -0.207051433               1
## 12                  Coprobacter_fastidiosus  0.145557806               1
## 13                        Coprococcus_comes -0.063292251               1
## 14                  Dysosmobacter_welbionis -0.064305792               1
## 15                    Enterocloster_hominis -0.031824969               1
## 16                         Escherichia_coli -0.300300259               1
## 17                      Eubacterium_ramulus -0.046621505               1
## 18                          GGB2653_SGB3574  0.213516163               1
## 19                          GGB3034_SGB4030  0.111313257               1
## 20                        GGB33586_SGB53517 -0.004922735               1
## 21                        GGB38744_SGB14842  0.317900636               1
## 22                         GGB9730_SGB15291 -0.040034023               1
## 23                         GGB9775_SGB15395 -0.154920380               1
## 24                         Guopingia_tenuis  0.210530302               1
## 25  Hydrogenoanaerobacterium_saccharovorans -0.186637026               1
## 26               Lachnoclostridium_sp_An138  0.010127428               1
## 27                Lachnospiraceae_bacterium  0.015302230               1
## 28    Lachnospiraceae_bacterium_CLA_AA_H215 -0.175695733               1
## 29    Lachnospiraceae_bacterium_CLA_AA_H244 -0.018895954               1
## 30           Lawsonibacter_asaccharolyticus -0.280783573               1
## 31                    Ligaoa_zhengdingensis  0.081559857               1
## 32                        Phocaeicola_dorei -0.047287220               1
## 33            Provencibacterium_massiliense  0.071582126               1
## 34                        Roseburia_hominis  0.304585688               1
## 35          Ruthenibacterium_lactatiformans -0.113547383               1
## 36                     Vescimonas_coprocola -0.015309680               1
## 37                    Youxingia_wuxianensis  0.040315222               1
## 38                bacterium_210917_DFI_7_65 -0.010704440               1
## 39                         GGB9708_SGB15233  0.221034267               1
## 40                         GGB9760_SGB15374 -0.001830135               1
## 41                  Segatella_brunsvicensis -0.076221089               1
## 42 Clostridiaceae_bacterium_Marseille_Q4149 -0.192744400               1
## 43                          GGB2970_SGB3952 -0.016739447               1
## 44                         GGB9787_SGB15410  0.016549069               1
## 45               Haemophilus_parainfluenzae  0.089464351               1
## 46                       Lactococcus_lactis  0.021571531               1
## 47         Mediterraneibacter_butyricigenes -0.124738294               1
## 48                    Ruminococcus_lactaris -0.066841896               1
## 49                          Roseburia_lenta  0.245591876               1
## 50             TM7_phylum_sp_oral_taxon_352  0.053481028               1
## 51                      Veillonella_parvula  0.003324881               1

elanet_microbiome_all$betas
## 285 x 1 sparse Matrix of class "dgCMatrix"
##                                                      s0
## (Intercept)                                 0.407222882
## Adlercreutzia_equolifaciens                 .          
## Agathobaculum_butyriciproducens             0.621419023
## Akkermansia_muciniphila                     .          
## Alistipes_communis                          .          
## Alistipes_finegoldii                        .          
## Alistipes_ihumii                            .          
## Alistipes_indistinctus                      .          
## Alistipes_onderdonkii                       .          
## Alistipes_putredinis                        .          
## Alistipes_senegalensis                      .          
## Alistipes_shahii                            .          
## Anaerobutyricum_hallii                      .          
## Anaerofilum_hominis                         0.084631010
## Anaeromassilibacillus_senegalensis          .          
## Anaerostipes_hadrus                         .          
## Anaerotignum_faecicola                     -0.193830429
## Anaerotruncus_colihominis                   0.093112698
## Anaerotruncus_massiliensis                  .          
## Anaerotruncus_rubiinfantis                  .          
## Bacteroides_caccae                          .          
## Bacteroides_cellulosilyticus                .          
## Bacteroides_clarus                          .          
## Bacteroides_eggerthii                       .          
## Bacteroides_fragilis                        .          
## Bacteroides_ovatus                          0.024651413
## Bacteroides_stercoris                       .          
## Bacteroides_thetaiotaomicron                .          
## Bacteroides_uniformis                       .          
## Bacteroides_xylanisolvens                   .          
## Barnesiella_intestinihominis               -0.095395373
## Bifidobacterium_adolescentis                .          
## Bifidobacterium_longum                      .          
## Bilophila_SGB15451                          .          
## Bilophila_wadsworthia                       .          
## Blautia_faecis                              .          
## Blautia_glucerasea                          .          
## Blautia_massiliensis                        .          
## Blautia_obeum                               .          
## Blautia_sp_MCC283                           .          
## Blautia_wexlerae                            .          
## Brotolimicola_acetigignens                  0.054915462
## Butyricimonas_faecihominis                  .          
## Butyricimonas_virosa                        .          
## Candidatus_Borkfalkia_ceftriaxoniphila      .          
## Candidatus_Cibionibacter_quicibialis        .          
## Clostridia_bacterium_UC5_1_1D1              0.082518832
## Clostridiaceae_bacterium                    .          
## Clostridiaceae_bacterium_AF18_31LB          .          
## Clostridiaceae_bacterium_Marseille_Q4143    .          
## Clostridiaceae_bacterium_Marseille_Q4145    .          
## Clostridiales_bacterium                     .          
## Clostridiales_bacterium_KLE1615             .          
## Clostridium_SGB4750                         .          
## Clostridium_SGB4909                         .          
## Clostridium_fessum                         -0.417582156
## Clostridium_leptum                          .          
## Clostridium_sp_AF20_17LB                    .          
## Clostridium_sp_AF27_2AA                     .          
## Clostridium_sp_AF36_4                       .          
## Clostridium_sp_AM22_11AC                    .          
## Clostridium_sp_AM33_3                       .          
## Collinsella_aerofaciens                    -0.207051433
## Coprobacter_fastidiosus                     0.145557806
## Coprococcus_catus                           .          
## Coprococcus_comes                          -0.063292251
## Coprococcus_eutactus                        .          
## Dorea_formicigenerans                       .          
## Dorea_longicatena                           .          
## Dorea_sp_AF36_15AT                          .          
## Dysosmobacter_SGB15077                      .          
## Dysosmobacter_welbionis                    -0.064305792
## Eggerthella_lenta                           .          
## Enterocloster_citroniae                     .          
## Enterocloster_hominis                      -0.031824969
## Escherichia_coli                           -0.300300259
## Eubacterium_ramulus                        -0.046621505
## Eubacterium_rectale                         .          
## Eubacterium_siraeum                         .          
## Eubacterium_ventriosum                      .          
## Faecalibacterium_SGB15346                   .          
## Faecalibacterium_prausnitzii                .          
## Faecalibacterium_sp_CLA_AA_H233             .          
## Faecalibacterium_sp_HTFF                    .          
## Faecalicatena_fissicatena                   .          
## Flavonifractor_plautii                      .          
## Fusicatenibacter_saccharivorans             .          
## Fusicatenibacter_sp_CLA_AA_H277             .          
## GGB13404_SGB14252                           .          
## GGB1420_SGB1957                             .          
## GGB2653_SGB3574                             0.213516163
## GGB2998_SGB3988                             .          
## GGB3034_SGB4030                             0.111313257
## GGB3109_SGB4121                             .          
## GGB3175_SGB4191                             .          
## GGB33469_SGB15236                           .          
## GGB33512_SGB15203                           .          
## GGB33586_SGB53517                          -0.004922735
## GGB3537_SGB4727                             .          
## GGB38744_SGB14842                           0.317900636
## GGB45432_SGB63101                           .          
## GGB45613_SGB63326                           .          
## GGB47687_SGB2286                            .          
## GGB52106_SGB72838                           .          
## GGB52130_SGB14966                           .          
## GGB9062_SGB13981                            .          
## GGB9063_SGB13982                            .          
## GGB9064_SGB13983                            .          
## GGB9342_SGB14306                            .          
## GGB9345_SGB14311                            .          
## GGB9453_SGB14844                            .          
## GGB9502_SGB14899                            .          
## GGB9509_SGB14906                            .          
## GGB9522_SGB14921                            .          
## GGB9531_SGB14932                            .          
## GGB9534_SGB14937                            .          
## GGB9602_SGB15031                            .          
## GGB9614_SGB15049                            .          
## GGB9619_SGB15067                            .          
## GGB9621_SGB15073                            .          
## GGB9635_SGB15106                            .          
## GGB9646_SGB15123                            .          
## GGB9667_SGB15164                            .          
## GGB9699_SGB15216                            .          
## GGB9708_SGB15234                            .          
## GGB9715_SGB15265                            .          
## GGB9719_SGB15272                            .          
## GGB9719_SGB15273                            .          
## GGB9730_SGB15291                           -0.040034023
## GGB9758_SGB15368                            .          
## GGB9760_SGB15373                            .          
## GGB9765_SGB15382                            .          
## GGB9770_SGB15390                            .          
## GGB9775_SGB15395                           -0.154920380
## GGB9781_SGB15402                            .          
## GGB9818_SGB15459                            .          
## Gemmiger_formicilis                         .          
## Guopingia_tenuis                            0.210530302
## Holdemania_filiformis                       .          
## Hydrogenoanaerobacterium_saccharovorans    -0.186637026
## Intestinimonas_butyriciproducens            .          
## Intestinimonas_gabonensis                   .          
## Intestinimonas_massiliensis                 .          
## Lachnoclostridium_sp_An138                  0.010127428
## Lachnospira_eligens                         .          
## Lachnospira_pectinoschiza                   .          
## Lachnospiraceae_bacterium                   0.015302230
## Lachnospiraceae_bacterium_AM48_27BH         .          
## Lachnospiraceae_bacterium_CLA_AA_H215      -0.175695733
## Lachnospiraceae_bacterium_CLA_AA_H244      -0.018895954
## Lachnotalea_sp_AF33_28                      .          
## Lacrimispora_amygdalina                     .          
## Lawsonibacter_SGB15145                      .          
## Lawsonibacter_asaccharolyticus             -0.280783573
## Lawsonibacter_hominis                       .          
## Ligaoa_zhengdingensis                       0.081559857
## Mediterraneibacter_faecis                   .          
## Odoribacter_splanchnicus                    .          
## Oliverpabstia_intestinalis                  .          
## Oscillibacter_sp_ER4                        .          
## Oscillibacter_sp_MSJ_31                     .          
## Oscillibacter_sp_PC13                       .          
## Oscillibacter_valericigenes                 .          
## Oscillospiraceae_bacterium                  .          
## Oscillospiraceae_bacterium_CLA_AA_H250      .          
## Oscillospiraceae_bacterium_Marseille_Q3528  .          
## Parabacteroides_distasonis                  .          
## Parabacteroides_merdae                      .          
## Paraprevotella_clara                        .          
## Parasutterella_excrementihominis            .          
## Phascolarctobacterium_faecium               .          
## Phocaeicola_dorei                          -0.047287220
## Phocaeicola_sartorii                        .          
## Phocaeicola_vulgatus                        .          
## Phocea_massiliensis                         .          
## Provencibacterium_massiliense               0.071582126
## Pseudoflavonifractor_capillosus             .          
## Roseburia_faecis                            .          
## Roseburia_hominis                           0.304585688
## Roseburia_intestinalis                      .          
## Roseburia_inulinivorans                     .          
## Ruminococcus_bicirculans                    .          
## Ruminococcus_bromii                         .          
## Ruminococcus_torques                        .          
## Ruthenibacterium_lactatiformans            -0.113547383
## Segatella_copri                             .          
## Simiaoa_sunii                               .          
## Streptococcus_salivarius                    .          
## Streptococcus_thermophilus                  .          
## Sutterella_wadsworthensis                   .          
## Vescimonas_coprocola                       -0.015309680
## Wansuia_hejianensis                         .          
## Youxingia_wuxianensis                       0.040315222
## bacterium_210917_DFI_7_65                  -0.010704440
## Bacteroides_faecis                          .          
## Clostridiaceae_unclassified_SGB4771         .          
## Clostridium_sp_AM49_4BH                     .          
## Colidextribacter_sp_210702_DFI_3_9          .          
## Enterocloster_lavalensis                    .          
## GGB2982_SGB3964                             .          
## GGB3304_SGB4367                             .          
## GGB3619_SGB4894                             .          
## GGB9296_SGB14253                            .          
## GGB9524_SGB14924                            .          
## GGB9574_SGB14987                            .          
## GGB9619_SGB15066                            .          
## GGB9707_SGB15229                            .          
## GGB9708_SGB15233                            0.221034267
## GGB9760_SGB15374                           -0.001830135
## Roseburia_sp_AF02_12                        .          
## Segatella_brunsvicensis                    -0.076221089
## Wujia_chipingensis                          .          
## Alistipes_dispar                            .          
## Alistipes_sp_AF17_16                        .          
## Anaerobutyricum_soehngenii                  .          
## Anaerosacchariphilus_sp_NSJ_68              .          
## Anaerotignum_sp_MSJ_24                      .          
## Bittarella_massiliensis                     .          
## Blautia_SGB4815                             .          
## Blautia_luti                                .          
## Blautia_sp_OF03_15BH                        .          
## Butyricimonas_paravirosa                    .          
## Catenibacillus_scindens                     .          
## Clostridiaceae_bacterium_Marseille_Q4149   -0.192744400
## Clostridium_SGB6173                         .          
## Clostridium_SGB6179                         .          
## Clostridium_sp_Marseille_P3244              .          
## Clostridium_sp_NSJ_42                       .          
## Coprobacter_secundus                        .          
## Eubacteriaceae_bacterium                    .          
## Faecalibacillus_faecis                      .          
## Faecalibacillus_intestinalis                .          
## GGB13489_SGB15224                           .          
## GGB2970_SGB3952                            -0.016739447
## GGB3352_SGB4436                             .          
## GGB34797_SGB14322                           .          
## GGB34900_SGB14891                           .          
## GGB3653_SGB4964                             .          
## GGB4456_SGB6141                             .          
## GGB4552_SGB6276                             .          
## GGB51441_SGB71759                           .          
## GGB58158_SGB79798                           .          
## GGB9365_SGB14341                            .          
## GGB9412_SGB14770                            .          
## GGB9627_SGB15081                            .          
## GGB9712_SGB15244                            .          
## GGB9747_SGB15356                            .          
## GGB9767_SGB15385                            .          
## GGB9787_SGB15410                            0.016549069
## GGB9790_SGB15413                            .          
## Haemophilus_parainfluenzae                  0.089464351
## Intestinibacter_bartlettii                  .          
## Lachnospira_sp_NSJ_43                       .          
## Lachnospiraceae_bacterium_OM04_12BH         .          
## Lactococcus_lactis                          0.021571531
## Lentihominibacter_faecis                    .          
## Massilioclostridium_coli                    .          
## Mediterraneibacter_butyricigenes           -0.124738294
## Mediterraneibacter_sp_NSJ_151               .          
## Methanobrevibacter_smithii                  .          
## Romboutsia_timonensis                       .          
## Ruminococcus_gnavus                         .          
## Ruminococcus_lactaris                      -0.066841896
## Ruminococcus_sp_AF41_9                      .          
## Senegalimassilia_anaerobia                  .          
## Slackia_isoflavoniconvertens                .          
## Streptococcus_parasanguinis                 .          
## Veillonella_dispar                          .          
## Victivallis_lenta                           .          
## Bifidobacterium_pseudocatenulatum           .          
## Eubacterium_sp_AF34_35BH                    .          
## Faecalicatena_contorta                      .          
## GGB9559_SGB14969                            .          
## GGB9759_SGB15370                            .          
## Roseburia_lenta                             0.245591876
## Enterocloster_bolteae                       .          
## GGB2848_SGB3813                             .          
## GGB3005_SGB3996                             .          
## GGB3061_SGB4063                             .          
## GGB36331_SGB15121                           .          
## Hungatella_hathewayi                        .          
## TM7_phylum_sp_oral_taxon_352                0.053481028
## Veillonella_parvula                         0.003324881
## GGB6649_SGB9391                             .          
## Veillonella_atypica                         .

5.6 Plot beta coefficients

Open code
data.frame(
  microbiome = row.names(elanet_microbiome_all$betas),
  beta = elanet_microbiome_all$betas[, 1]
) %>%
  arrange(abs(beta)) %>%
  filter(abs(beta) > 0,
         !grepl('Intercept', microbiome)) %>%
  mutate(microbiome = factor(microbiome, levels = microbiome)) %>% # Preserve order
  ggplot(
    aes(
      x = microbiome,
      y = beta
    )
  ) +
  geom_point() +
  geom_hline(yintercept = 0, color = "black") +
  labs(
    y = "Standardized beta coefficients",
    x = "Bacteria species"
  ) +
  theme_minimal() +
  coord_flip() + # Flip coordinates to have outcomes on the y-axis
  theme(
    axis.text.x = element_text(size = 10),
    axis.text.y = element_text(size = 10),
    axis.title.x = element_text(size = 12),
    axis.title.y = element_text(size = 12),
    legend.position = "bottom"
  )

Regression coefficients from the elastic net model predicting vegan diet strategy based on CLR-transformed and standardized read counts across bacterial taxa. Taxa are ordered by the magnitude of the standardized coefficients, indicating their relative importance in distinguishing between the diet groups. The sign of each coefficient indicates the direction of association with vegan diet status, with positive values indicating a higher likelihood of vegan status and negative values indicating omnivore status. Taxa whose effects were shrunk to zero are not shown.

6 External validation

External validation was performed with an independent Czech cohort.

As a first step, we will use the previously developed and validated elastic net model to predict vegan status in the independent Czech cohort. The validation data will be standardized using the mean and standard deviation of each taxa as taken from the training cohort to ensure comparability across datasets. For each subject in the external validation cohort, we will estimate the predicted probability of being vegan using the elastic net model. This predicted probability will then be used as a variable to discriminate between the diet groups in the independent cohort.

In a 2nd step, we will look at taxa that significantly differed between diet groups (average vegan diet effect across both countries, FDR<0.01) estimated by linear models (one per a taxa) with data of training cohort. Then we will fit linear models also for external validation cohort. Effect of vegan diet on these taxa will be shown along with 95% confidence interval for all cohorts: training Czech and Italian cohorts, but also in Czech independent (validating) cohort

6.1 Prediction of diet (elastic net)

6.1.1 Get table of weights, means and SDs

Open code

coefs_microbiome_all <- get_coef(
  original_data = data_analysis,
  glmnet_model = elanet_microbiome_all)

coefs_microbiome_all
## # A tibble: 285 × 5
##    predictor                       beta_scaled beta_OrigScale    mean    SD
##    <chr>                                 <dbl>          <dbl>   <dbl> <dbl>
##  1 (Intercept)                           0.407          NA    NA      NA   
##  2 Adlercreutzia_equolifaciens           0               0    -0.936   1.48
##  3 Agathobaculum_butyriciproducens       0.621           1.30  1.63    1.04
##  4 Akkermansia_muciniphila               0               0     1.44    2.26
##  5 Alistipes_communis                    0               0     1.67    1.78
##  6 Alistipes_finegoldii                  0               0     0.888   1.87
##  7 Alistipes_ihumii                      0               0     0.838   1.49
##  8 Alistipes_indistinctus                0               0    -0.0519  1.48
##  9 Alistipes_onderdonkii                 0               0     1.83    2.40
## 10 Alistipes_putredinis                  0               0     2.96    2.72
## # ℹ 275 more rows

6.1.2 Identify shared and missing predictors

Open code

## Which are missing in the validation set
missing <- setdiff(
  coefs_microbiome_all$predictor[-1], 
  colnames(
    data_microbiome_validation
    )
  )

missing
## character(0)

## Which are common with the validations et
common_predictors <- intersect(coefs_microbiome_all$predictor, colnames(data_microbiome_validation))

6.1.3 Standardize data in validation set

Open code
data_microbiome_validation_pred_all <- data_microbiome_validation %>%
  dplyr::mutate(
    vegan = if_else(
      Diet == "VEGAN", 1, 0
    )
  ) %>%
  dplyr::select(
    vegan,
    dplyr::all_of(common_predictors)
  ) %>% 
  dplyr::mutate(
    across(
      .cols = -vegan,
      .fns = ~ . 
      - coefs_microbiome_all$mean[
        match(
          cur_column(), 
          coefs_microbiome_all$predictor
          )
        ]
      )
    ) %>% 
  dplyr::mutate(
    across(
      .cols = -vegan,
      .fns = ~ . 
      / coefs_microbiome_all$SD[
        match(
          cur_column(), 
          coefs_microbiome_all$predictor
          )
        ]
      )
    ) 

6.1.4 Result

Open code
elanet_microbiome_all$fit
## 
## Call:  glmnet::glmnet(x = original_predictors, y = original_outcome,      family = family, alpha = optim_par$alpha[1], lambda = optim_par$lamb_1se[1],      standardize = standardize) 
## 
##   Df  %Dev  Lambda
## 1 50 40.65 0.05672

newx <- as.matrix(data_microbiome_validation_pred_all[,-1])

predicted <- predict(
  elanet_microbiome_all$fit, 
  newx = newx)

tr <- data_microbiome_validation_pred_all %>% 
  dplyr::mutate(
    predicted_logit = as.numeric(
      predict(
        elanet_microbiome_all$fit,
        newx = newx
        )
      )
    ) %>% 
  dplyr::mutate(
    predicted = inv_logit(predicted_logit)
  )

roc_microbiome_all <- pROC::roc(
      vegan ~ predicted_logit,
      data = tr,
      direction = "<",
      levels = c(0, 1),
      ci = TRUE
      )

roc_microbiome_all
## 
## Call:
## roc.formula(formula = vegan ~ predicted_logit, data = tr, direction = "<",     levels = c(0, 1), ci = TRUE)
## 
## Data: predicted_logit in 43 controls (vegan 0) < 58 cases (vegan 1).
## Area under the curve: 0.8372
## 95% CI: 0.7584-0.916 (DeLong)
plot(roc_microbiome_all)

Receiver Operating Characteristic (ROC) curve illustrating the model’s ability to distinguish between vegan and omnivore status based on CLR-transformed bacterial taxa abundances in the external validation Czech cohort. The curve plots the true positive rate (sensitivity) against the true positive rate (specificity) at various thresholds of predicted vegan status, as estimated from the elastic net model developed on the training data. The area under the curve (AUC) represents the model’s overall performance, with values closer to 1 indicating stronger discrimination.

6.2 Diet effect across datasets

Similarly as in training data cohorts, we will fit linear model per each of the selected taxa (\(CLR\) - transformed), with a single fixed effect factor of diet.

6.2.1 Linear models in validation cohort

Open code
data_analysis_microbiome <- data_microbiome_validation %>%
  dplyr::mutate(
    Diet_VEGAN = as.numeric(
      dplyr::if_else(
        Diet == 'VEGAN', 1, 0
      )
    )
  ) %>%
  dplyr::select(
    Diet_VEGAN,
    all_of(common_microbiome)
  )

6.2.1.1 Define number of microbiome and covariates

Open code
n_covarites <- 1
n_features <- ncol(data_analysis_microbiome) - n_covarites

6.2.1.2 Create empty objects

Open code
outcome <- vector('double', n_features)
logFD_VGdiet <- vector('double', n_features)
P_VGdiet <- vector('double', n_features)
CI_L_VGdiet <- vector('double', n_features)
CI_U_VGdiet <- vector('double', n_features)

6.2.1.3 Estimate over outcomes

Open code
for (i in 1:n_features) {
  ## define variable
  data_analysis_microbiome$outcome <- data_analysis_microbiome[, (i + n_covarites)]

  ## fit model
  model <- lm(outcome ~ Diet_VEGAN, data = data_analysis_microbiome)

  ## save results
  outcome[i] <- names(data_analysis_microbiome)[i + n_covarites]

  ## diet effect
  tr <- confint(model)

  CI_L_VGdiet[i] <- tr[which(row.names(tr) == "Diet_VEGAN"), ][1]
  CI_U_VGdiet[i] <- tr[which(row.names(tr) == "Diet_VEGAN"), ][2]

  logFD_VGdiet[i] <- summary(model)$coefficients[
    which(
      names(model$coefficients) == "Diet_VEGAN"
    ), 1
  ]

  P_VGdiet[i] <- summary(model)$coefficients[
    which(
      names(model$coefficients) == "Diet_VEGAN"
    ), 4
  ]
}

6.2.1.4 Results table

Open code

result_microbiome_val <- data.frame(
  outcome,
  logFD_VGdiet, P_VGdiet,
  CI_L_VGdiet, CI_U_VGdiet
)

kableExtra::kable(result_microbiome_val,
  caption = "Results of linear models estimating the effect of diet on CLR-trasformed taxa count. Only lipids that significantly differed between diet groups in training cohorts (FDR < 0.1, average effect across both training cohorts) were included. `logFD` represents the estimated effects (regression coefficient), indicating how much the CLR-transformed taxa count differ between vegans and omnivores. `P`: p-value, `fdr`: p-value adjusted for multiple comparisons, and `CI_L` and `CI_U` represent the lower and upper bounds of the 95% confidence interval, respectively. All estimates in a single row are based on a single model."
)
Results of linear models estimating the effect of diet on CLR-trasformed taxa count. Only lipids that significantly differed between diet groups in training cohorts (FDR < 0.1, average effect across both training cohorts) were included. logFD represents the estimated effects (regression coefficient), indicating how much the CLR-transformed taxa count differ between vegans and omnivores. P: p-value, fdr: p-value adjusted for multiple comparisons, and CI_L and CI_U represent the lower and upper bounds of the 95% confidence interval, respectively. All estimates in a single row are based on a single model.
outcome logFD_VGdiet P_VGdiet CI_L_VGdiet CI_U_VGdiet
Adlercreutzia_equolifaciens -0.1712072 0.4895466 -0.6609763 0.3185619
Agathobaculum_butyriciproducens 0.5537807 0.0008637 0.2340022 0.8735593
Akkermansia_muciniphila -0.1277027 0.7334571 -0.8697112 0.6143058
Alistipes_communis -0.0188421 0.9380698 -0.4988149 0.4611307
Alistipes_finegoldii -0.2539928 0.4124540 -0.8663162 0.3583306
Alistipes_ihumii 0.5023615 0.0218233 0.0745966 0.9301264
Alistipes_indistinctus 0.2501329 0.4332701 -0.3806615 0.8809272
Alistipes_onderdonkii 0.2929591 0.3125723 -0.2797356 0.8656537
Alistipes_putredinis -0.4535196 0.2490353 -1.2296037 0.3225646
Alistipes_senegalensis 0.1223145 0.5738555 -0.3078061 0.5524352
Alistipes_shahii 0.1102602 0.6246611 -0.3355110 0.5560314
Anaerobutyricum_hallii -0.1045680 0.6387499 -0.5451855 0.3360494
Anaerofilum_hominis 1.0367586 0.0173732 0.1864692 1.8870479
Anaeromassilibacillus_senegalensis -0.0320458 0.9302484 -0.7566266 0.6925350
Anaerostipes_hadrus 0.2206812 0.1562736 -0.0858334 0.5271958
Anaerotignum_faecicola -0.5252774 0.0274779 -0.9910399 -0.0595148
Anaerotruncus_colihominis -0.7721826 0.0133008 -1.3799612 -0.1644040
Anaerotruncus_massiliensis 0.2777109 0.1667675 -0.1178920 0.6733138
Anaerotruncus_rubiinfantis 0.9606116 0.0070677 0.2677258 1.6534974
Bacteroides_caccae -0.1387429 0.5256803 -0.5710077 0.2935220
Bacteroides_cellulosilyticus 0.5612561 0.0519699 -0.0048823 1.1273944
Bacteroides_clarus -0.1340533 0.3263691 -0.4037269 0.1356203
Bacteroides_eggerthii -0.1177902 0.6885696 -0.6992239 0.4636435
Bacteroides_fragilis -0.0775871 0.7252147 -0.5143274 0.3591531
Bacteroides_ovatus 0.6884843 0.0113963 0.1586691 1.2182996
Bacteroides_stercoris -0.3655674 0.1282080 -0.8384118 0.1072769
Bacteroides_thetaiotaomicron 0.1316828 0.6434847 -0.4311276 0.6944933
Bacteroides_uniformis -0.2030937 0.4686614 -0.7570518 0.3508643
Bacteroides_xylanisolvens 0.3189791 0.3004004 -0.2890032 0.9269613
Barnesiella_intestinihominis -0.6391749 0.0045553 -1.0760364 -0.2023135
Bifidobacterium_adolescentis 0.6577163 0.0545191 -0.0129987 1.3284313
Bifidobacterium_longum 0.7509240 0.0024420 0.2718638 1.2299841
Bilophila_SGB15451 -0.0646024 0.2053893 -0.1651612 0.0359564
Bilophila_wadsworthia 0.2377731 0.3187289 -0.2330223 0.7085684
Blautia_faecis -0.0867731 0.6701776 -0.4898292 0.3162831
Blautia_glucerasea -0.4687770 0.0434679 -0.9235313 -0.0140228
Blautia_massiliensis -0.6766600 0.0134021 -1.2098558 -0.1434643
Blautia_obeum -0.1130708 0.6471065 -0.6016671 0.3755254
Blautia_sp_MCC283 0.3521311 0.2594842 -0.2639469 0.9682091
Blautia_wexlerae -0.2687129 0.0377658 -0.5219303 -0.0154955
Brotolimicola_acetigignens -0.6579227 0.0453567 -1.3019769 -0.0138685
Butyricimonas_faecihominis 0.2836388 0.1439125 -0.0984288 0.6657063
Butyricimonas_virosa 0.1704732 0.1459978 -0.0603651 0.4013115
Candidatus_Borkfalkia_ceftriaxoniphila 0.0508793 0.8424411 -0.4556856 0.5574443
Candidatus_Cibionibacter_quicibialis -0.2883849 0.1897526 -0.7217588 0.1449889
Clostridia_bacterium_UC5_1_1D1 -0.3502745 0.3140671 -1.0371424 0.3365933
Clostridiaceae_bacterium 0.2940025 0.1167047 -0.0746116 0.6626167
Clostridiaceae_bacterium_AF18_31LB -0.2764914 0.0301573 -0.5259015 -0.0270813
Clostridiaceae_bacterium_Marseille_Q4143 -0.1494612 0.2024401 -0.3805852 0.0816627
Clostridiaceae_bacterium_Marseille_Q4145 0.3719162 0.0296333 0.0375238 0.7063085
Clostridiales_bacterium 0.2111988 0.4089236 -0.2941174 0.7165149
Clostridiales_bacterium_KLE1615 0.2199507 0.2351468 -0.1454236 0.5853250
Clostridium_SGB4750 0.0675850 0.7080028 -0.2894331 0.4246030
Clostridium_SGB4909 0.5328757 0.1363158 -0.1711445 1.2368959
Clostridium_fessum -0.3313288 0.0327545 -0.6349262 -0.0277315
Clostridium_leptum 0.9120195 0.0053713 0.2763156 1.5477234
Clostridium_sp_AF20_17LB 0.3906820 0.0805226 -0.0483397 0.8297037
Clostridium_sp_AF27_2AA 0.7160025 0.0009135 0.3004896 1.1315155
Clostridium_sp_AF36_4 -0.4404313 0.1702251 -1.0729976 0.1921350
Clostridium_sp_AM22_11AC 0.0384912 0.8289564 -0.3140973 0.3910798
Clostridium_sp_AM33_3 0.1253889 0.3773539 -0.1551798 0.4059577
Collinsella_aerofaciens -0.0748634 0.8080372 -0.6846304 0.5349036
Coprobacter_fastidiosus 0.4436160 0.0610310 -0.0209238 0.9081557
Coprococcus_catus -0.4613416 0.0012003 -0.7357998 -0.1868834
Coprococcus_comes -1.0673442 0.0000000 -1.3713852 -0.7633031
Coprococcus_eutactus 0.4381462 0.3634368 -0.5140267 1.3903190
Dorea_formicigenerans -0.4849885 0.0000141 -0.6955631 -0.2744139
Dorea_longicatena -0.7243893 0.0000019 -1.0080790 -0.4406996
Dorea_sp_AF36_15AT -0.2449941 0.1043677 -0.5415733 0.0515851
Dysosmobacter_SGB15077 -0.3991065 0.0441083 -0.7874769 -0.0107360
Dysosmobacter_welbionis -0.3426355 0.2319397 -0.9078904 0.2226193
Eggerthella_lenta -0.4342056 0.1261006 -0.9926894 0.1242782
Enterocloster_citroniae -0.1039522 0.7343712 -0.7101222 0.5022177
Enterocloster_hominis 0.5173151 0.0581160 -0.0181277 1.0527578
Escherichia_coli 0.0267410 0.9252341 -0.5372348 0.5907169
Eubacterium_ramulus -0.2603367 0.1011099 -0.5724773 0.0518040
Eubacterium_rectale -0.0129466 0.9645861 -0.5900731 0.5641798
Eubacterium_siraeum -0.0140950 0.9710428 -0.7825936 0.7544037
Eubacterium_ventriosum -0.1389631 0.6478496 -0.7408047 0.4628784
Faecalibacterium_SGB15346 -0.2533722 0.2401229 -0.6787848 0.1720405
Faecalibacterium_prausnitzii -0.2262934 0.1740079 -0.5542123 0.1016256
Faecalibacterium_sp_CLA_AA_H233 -0.6906235 0.0215382 -1.2773849 -0.1038621
Faecalibacterium_sp_HTFF -0.4697997 0.1064197 -1.0419248 0.1023254
Faecalicatena_fissicatena 0.0967373 0.7096708 -0.4173568 0.6108313
Flavonifractor_plautii -0.2384383 0.4519574 -0.8649620 0.3880853
Fusicatenibacter_saccharivorans 0.2304512 0.2259058 -0.1447982 0.6057006
Fusicatenibacter_sp_CLA_AA_H277 0.0242508 0.8934732 -0.3341621 0.3826637
GGB13404_SGB14252 0.2038157 0.3857088 -0.2603452 0.6679765
GGB1420_SGB1957 -0.3330708 0.0511249 -0.6678015 0.0016600
GGB2653_SGB3574 0.0456495 0.8480939 -0.4259832 0.5172822
GGB2998_SGB3988 -0.0336482 0.8763545 -0.4616444 0.3943480
GGB3034_SGB4030 0.6962316 0.0167594 0.1284732 1.2639899
GGB3109_SGB4121 -0.4282785 0.0133457 -0.7655423 -0.0910147
GGB3175_SGB4191 -0.5151292 0.0490286 -1.0280226 -0.0022359
GGB33469_SGB15236 0.0547046 0.8410499 -0.4851140 0.5945232
GGB33512_SGB15203 -0.3457539 0.2536613 -0.9432656 0.2517579
GGB33586_SGB53517 0.5332804 0.0751835 -0.0551460 1.1217067
GGB3537_SGB4727 0.1435250 0.6343154 -0.4533352 0.7403852
GGB38744_SGB14842 1.0430771 0.0015441 0.4075608 1.6785934
GGB45432_SGB63101 0.2514547 0.3905059 -0.3270381 0.8299474
GGB45613_SGB63326 0.3088180 0.4541052 -0.5065140 1.1241501
GGB47687_SGB2286 0.0738015 0.6715738 -0.2705524 0.4181554
GGB52106_SGB72838 0.3734460 0.1885440 -0.1862099 0.9331018
GGB52130_SGB14966 0.6001682 0.0216521 0.0898028 1.1105335
GGB9062_SGB13981 0.2870239 0.4246162 -0.4233169 0.9973647
GGB9063_SGB13982 0.1213392 0.6274187 -0.3731619 0.6158403
GGB9064_SGB13983 -0.1060654 0.6944834 -0.6403210 0.4281902
GGB9342_SGB14306 -0.1090269 0.6337649 -0.5616879 0.3436340
GGB9345_SGB14311 -0.6261437 0.0136545 -1.1209108 -0.1313765
GGB9453_SGB14844 -0.1624281 0.3976526 -0.5418189 0.2169627
GGB9502_SGB14899 -0.3142442 0.0637990 -0.6468678 0.0183795
GGB9509_SGB14906 -0.2012361 0.3732921 -0.6476902 0.2452180
GGB9522_SGB14921 -0.0856743 0.6497963 -0.4589391 0.2875904
GGB9531_SGB14932 0.0832237 0.7472669 -0.4277969 0.5942442
GGB9534_SGB14937 0.9503439 0.0020320 0.3554000 1.5452879
GGB9602_SGB15031 -0.2983810 0.2842465 -0.8482758 0.2515138
GGB9614_SGB15049 -0.1057539 0.5933164 -0.4974092 0.2859014
GGB9619_SGB15067 -0.0658281 0.8156820 -0.6246809 0.4930247
GGB9621_SGB15073 0.6829391 0.0332750 0.0552563 1.3106219
GGB9635_SGB15106 -0.7209995 0.0278304 -1.3617952 -0.0802037
GGB9646_SGB15123 0.1659579 0.6161645 -0.4888612 0.8207769
GGB9667_SGB15164 0.1939356 0.4905662 -0.3621603 0.7500315
GGB9699_SGB15216 -0.1154958 0.7079297 -0.7254431 0.4944515
GGB9708_SGB15234 -0.3044069 0.2555122 -0.8325325 0.2237187
GGB9715_SGB15265 -0.0395713 0.8828052 -0.5708351 0.4916925
GGB9719_SGB15272 0.0933414 0.7784423 -0.5631568 0.7498397
GGB9719_SGB15273 0.3419837 0.1182284 -0.0885956 0.7725630
GGB9730_SGB15291 -0.3397912 0.0556582 -0.6879557 0.0083733
GGB9758_SGB15368 0.0479382 0.8890711 -0.6322707 0.7281472
GGB9760_SGB15373 -0.2738247 0.1788212 -0.6751025 0.1274531
GGB9765_SGB15382 0.3559094 0.1954146 -0.1858484 0.8976672
GGB9770_SGB15390 0.2845921 0.2368495 -0.1898957 0.7590799
GGB9775_SGB15395 -0.1485127 0.4852481 -0.5691760 0.2721506
GGB9781_SGB15402 0.5571759 0.0295710 0.0564116 1.0579401
GGB9818_SGB15459 -0.1679343 0.5833727 -0.7734864 0.4376179
Gemmiger_formicilis -0.3194152 0.2837946 -0.9075192 0.2686887
Guopingia_tenuis 0.3191492 0.4287082 -0.4777396 1.1160380
Holdemania_filiformis 0.8843009 0.0014772 0.3478156 1.4207862
Hydrogenoanaerobacterium_saccharovorans -0.4185804 0.0049499 -0.7074932 -0.1296677
Intestinimonas_butyriciproducens 0.0089281 0.9803592 -0.7088469 0.7267031
Intestinimonas_gabonensis -0.1831603 0.6305360 -0.9364266 0.5701061
Intestinimonas_massiliensis 0.6341853 0.0285001 0.0680849 1.2002857
Lachnoclostridium_sp_An138 -0.0435669 0.8425183 -0.4775438 0.3904100
Lachnospira_eligens 0.0924010 0.7642934 -0.5173738 0.7021757
Lachnospira_pectinoschiza 0.0255369 0.9434809 -0.6873761 0.7384499
Lachnospiraceae_bacterium -0.3042466 0.1525318 -0.7229708 0.1144776
Lachnospiraceae_bacterium_AM48_27BH 0.0756174 0.6192999 -0.2254218 0.3766565
Lachnospiraceae_bacterium_CLA_AA_H215 -0.3672498 0.1048809 -0.8124932 0.0779937
Lachnospiraceae_bacterium_CLA_AA_H244 -0.2604068 0.2598342 -0.7163438 0.1955301
Lachnotalea_sp_AF33_28 0.5603215 0.1053793 -0.1199840 1.2406270
Lacrimispora_amygdalina 0.2502885 0.2215733 -0.1534390 0.6540161
Lawsonibacter_SGB15145 -0.4051988 0.0175845 -0.7381619 -0.0722358
Lawsonibacter_asaccharolyticus -0.8174813 0.0048166 -1.3798964 -0.2550663
Lawsonibacter_hominis -0.0136630 0.9671727 -0.6707464 0.6434203
Ligaoa_zhengdingensis -0.1598639 0.6505451 -0.8579574 0.5382297
Mediterraneibacter_faecis -1.4644428 0.0000000 -1.8413197 -1.0875658
Odoribacter_splanchnicus -0.6821452 0.0000286 -0.9905626 -0.3737278
Oliverpabstia_intestinalis -0.8044961 0.0000562 -1.1836306 -0.4253617
Oscillibacter_sp_ER4 -0.2381552 0.3320725 -0.7229604 0.2466500
Oscillibacter_sp_MSJ_31 -0.4765347 0.0830886 -1.0166200 0.0635506
Oscillibacter_sp_PC13 0.7156796 0.0971098 -0.1321697 1.5635290
Oscillibacter_valericigenes -0.0959740 0.7011394 -0.5907381 0.3987902
Oscillospiraceae_bacterium -0.8911802 0.0023796 -1.4581893 -0.3241711
Oscillospiraceae_bacterium_CLA_AA_H250 -0.3197186 0.2250654 -0.8393750 0.1999378
Oscillospiraceae_bacterium_Marseille_Q3528 -0.0646419 0.6990623 -0.3954645 0.2661807
Parabacteroides_distasonis -0.3658317 0.0505524 -0.7325608 0.0008974
Parabacteroides_merdae -0.2503076 0.2058630 -0.6403422 0.1397270
Paraprevotella_clara -0.0364840 0.8481744 -0.4136241 0.3406562
Parasutterella_excrementihominis 0.2896829 0.3987431 -0.3885143 0.9678801
Phascolarctobacterium_faecium 0.0017026 0.9949541 -0.5311556 0.5345608
Phocaeicola_dorei -0.2834248 0.3845410 -0.9272939 0.3604443
Phocaeicola_sartorii 0.0000000 NaN 0.0000000 0.0000000
Phocaeicola_vulgatus -0.1565157 0.6106139 -0.7644806 0.4514493
Phocea_massiliensis 0.0674568 0.8597579 -0.6881407 0.8230542
Provencibacterium_massiliense 0.3298768 0.3869191 -0.4232944 1.0830479
Pseudoflavonifractor_capillosus -0.0051894 0.9892089 -0.7645954 0.7542166
Roseburia_faecis 0.4290783 0.2610326 -0.3240827 1.1822392
Roseburia_hominis 1.2752450 0.0001261 0.6412974 1.9091926
Roseburia_intestinalis -0.6589740 0.0670335 -1.3650660 0.0471180
Roseburia_inulinivorans -0.4382647 0.1540169 -1.0436397 0.1671102
Ruminococcus_bicirculans -0.1796234 0.6298917 -0.9169524 0.5577056
Ruminococcus_bromii -0.5545669 0.1901062 -1.3886202 0.2794864
Ruminococcus_torques -0.3437329 0.2409635 -0.9219013 0.2344355
Ruthenibacterium_lactatiformans 0.0673499 0.8131221 -0.4964434 0.6311432
Segatella_copri -0.3326160 0.5795627 -1.5199399 0.8547079
Simiaoa_sunii -0.8033900 0.0368014 -1.5565334 -0.0502465
Streptococcus_salivarius -0.9700788 0.0059191 -1.6543357 -0.2858219
Streptococcus_thermophilus -0.4850060 0.0969138 -1.0592397 0.0892278
Sutterella_wadsworthensis -0.5994318 0.0097883 -1.0509554 -0.1479083
Vescimonas_coprocola -0.2536396 0.3344338 -0.7725060 0.2652269
Wansuia_hejianensis 0.1636774 0.4748630 -0.2890765 0.6164313
Youxingia_wuxianensis 0.9952571 0.0074120 0.2729631 1.7175511
bacterium_210917_DFI_7_65 0.0132664 0.9490081 -0.3973007 0.4238335
Bacteroides_faecis 0.1426993 0.4396300 -0.2222049 0.5076035
Clostridiaceae_unclassified_SGB4771 0.2898282 0.1623543 -0.1186999 0.6983563
Clostridium_sp_AM49_4BH -0.1319839 0.6414443 -0.6926274 0.4286595
Colidextribacter_sp_210702_DFI_3_9 -0.0469760 0.8580027 -0.5665904 0.4726384
Enterocloster_lavalensis -0.1157850 0.6102710 -0.5651044 0.3335345
GGB2982_SGB3964 -0.1414619 0.1574043 -0.3384871 0.0555632
GGB3304_SGB4367 -0.2141347 0.3447208 -0.6616619 0.2333925
GGB3619_SGB4894 -0.1425176 0.5727179 -0.6421960 0.3571607
GGB9296_SGB14253 0.1413539 0.4128722 -0.1997268 0.4824345
GGB9524_SGB14924 -0.4280648 0.0233726 -0.7968804 -0.0592492
GGB9574_SGB14987 -0.6708302 0.0079814 -1.1624111 -0.1792493
GGB9619_SGB15066 0.7867548 0.0027338 0.2788275 1.2946820
GGB9707_SGB15229 0.1067650 0.6112393 -0.3086787 0.5222086
GGB9708_SGB15233 0.0740248 0.7873171 -0.4689180 0.6169677
GGB9760_SGB15374 -0.0883561 0.6231081 -0.4439741 0.2672618
Roseburia_sp_AF02_12 -0.7572841 0.0689237 -1.5744006 0.0598324
Segatella_brunsvicensis -0.4376605 0.1411815 -1.0231361 0.1478151
Wujia_chipingensis -0.3435443 0.2324910 -0.9109729 0.2238842
Alistipes_dispar 0.1980443 0.2570647 -0.1466802 0.5427688
Alistipes_sp_AF17_16 -0.0135480 0.9428643 -0.3876781 0.3605821
Anaerobutyricum_soehngenii -0.2252784 0.5383520 -0.9492191 0.4986624
Anaerosacchariphilus_sp_NSJ_68 0.5567885 0.0518067 -0.0044448 1.1180218
Anaerotignum_sp_MSJ_24 0.3290706 0.1092091 -0.0749030 0.7330441
Bittarella_massiliensis 1.0542704 0.0050189 0.3253885 1.7831524
Blautia_SGB4815 -1.0178179 0.0001166 -1.5210841 -0.5145517
Blautia_luti 0.0602180 0.7820664 -0.3705466 0.4909826
Blautia_sp_OF03_15BH 0.0468998 0.8402839 -0.4136520 0.5074517
Butyricimonas_paravirosa 0.6661290 0.0011973 0.2699331 1.0623250
Catenibacillus_scindens 0.8575408 0.0104144 0.2060001 1.5090815
Clostridiaceae_bacterium_Marseille_Q4149 -0.2451357 0.2656415 -0.6796228 0.1893515
Clostridium_SGB6173 -0.1714187 0.6231528 -0.8614376 0.5186003
Clostridium_SGB6179 -0.0567863 0.8481564 -0.6437244 0.5301517
Clostridium_sp_Marseille_P3244 0.0920410 0.8388431 -0.8035997 0.9876817
Clostridium_sp_NSJ_42 0.0610109 0.7988062 -0.4126544 0.5346763
Coprobacter_secundus 0.8334583 0.0001341 0.4173651 1.2495515
Eubacteriaceae_bacterium -0.0459075 0.8802065 -0.6487671 0.5569521
Faecalibacillus_faecis 0.2289766 0.3322933 -0.2373579 0.6953112
Faecalibacillus_intestinalis 0.0074233 0.9763810 -0.4888300 0.5036766
GGB13489_SGB15224 -0.1187886 0.6059785 -0.5742734 0.3366962
GGB2970_SGB3952 0.1460377 0.3704544 -0.1760309 0.4681062
GGB3352_SGB4436 0.5920488 0.0295483 0.0600183 1.1240793
GGB34797_SGB14322 -0.8256021 0.0001124 -1.2327896 -0.4184145
GGB34900_SGB14891 0.7211672 0.0382694 0.0397665 1.4025679
GGB3653_SGB4964 0.0655478 0.8033933 -0.4554745 0.5865700
GGB4456_SGB6141 0.2806543 0.2430794 -0.1935551 0.7548637
GGB4552_SGB6276 0.0736109 0.7693499 -0.4231396 0.5703614
GGB51441_SGB71759 0.2405052 0.2167575 -0.1433775 0.6243878
GGB58158_SGB79798 0.5889548 0.1781303 -0.2727474 1.4506571
GGB9365_SGB14341 -0.0567238 0.8336735 -0.5912952 0.4778475
GGB9412_SGB14770 0.5980316 0.0018600 0.2269535 0.9691097
GGB9627_SGB15081 0.2596162 0.2650512 -0.1999651 0.7191975
GGB9712_SGB15244 -0.2739057 0.0943491 -0.5956694 0.0478579
GGB9747_SGB15356 -0.4817909 0.0318036 -0.9207757 -0.0428060
GGB9767_SGB15385 0.4391785 0.0151973 0.0864618 0.7918952
GGB9787_SGB15410 0.6099757 0.0062157 0.1771002 1.0428511
GGB9790_SGB15413 -0.0550261 0.7687885 -0.4254316 0.3153795
Haemophilus_parainfluenzae 0.2149287 0.4472719 -0.3439962 0.7738537
Intestinibacter_bartlettii -0.7170859 0.0142129 -1.2871425 -0.1470294
Lachnospira_sp_NSJ_43 0.6837830 0.0050380 0.2108276 1.1567383
Lachnospiraceae_bacterium_OM04_12BH 0.2308796 0.4846970 -0.4222615 0.8840206
Lactococcus_lactis 1.0243734 0.0001764 0.5029699 1.5457770
Lentihominibacter_faecis 0.4104142 0.0613862 -0.0199581 0.8407866
Massilioclostridium_coli 0.7560415 0.0677404 -0.0561873 1.5682702
Mediterraneibacter_butyricigenes 0.2926664 0.1789369 -0.1363383 0.7216712
Mediterraneibacter_sp_NSJ_151 -0.0661280 0.7868718 -0.5501119 0.4178559
Methanobrevibacter_smithii -0.1398588 0.6387379 -0.7291598 0.4494422
Romboutsia_timonensis -0.4420490 0.2203266 -1.1531583 0.2690602
Ruminococcus_gnavus -0.2896922 0.2618347 -0.7990501 0.2196657
Ruminococcus_lactaris -0.5709585 0.0153996 -1.0304470 -0.1114699
Ruminococcus_sp_AF41_9 0.3716328 0.0953338 -0.0662553 0.8095209
Senegalimassilia_anaerobia -0.2760952 0.0044868 -0.4644656 -0.0877247
Slackia_isoflavoniconvertens -0.3934137 0.0092664 -0.6875335 -0.0992939
Streptococcus_parasanguinis -0.3339438 0.2667054 -0.9271643 0.2592768
Veillonella_dispar 0.1429699 0.6546016 -0.4892106 0.7751504
Victivallis_lenta 0.2228559 0.3279291 -0.2269162 0.6726281
Bifidobacterium_pseudocatenulatum 0.1556873 0.6136983 -0.4543332 0.7657078
Eubacterium_sp_AF34_35BH 0.2268773 0.2467866 -0.1595118 0.6132664
Faecalicatena_contorta -0.6498984 0.0681419 -1.3491323 0.0493355
GGB9559_SGB14969 0.2890652 0.1298004 -0.0864046 0.6645350
GGB9759_SGB15370 0.2873475 0.1206768 -0.0768754 0.6515704
Roseburia_lenta 0.2487548 0.2102571 -0.1426542 0.6401638
Enterocloster_bolteae -0.2708939 0.4398033 -0.9638748 0.4220870
GGB2848_SGB3813 -0.2851155 0.2844685 -0.8108065 0.2405756
GGB3005_SGB3996 0.1700297 0.4494938 -0.2743112 0.6143706
GGB3061_SGB4063 0.2825993 0.2147087 -0.1664476 0.7316462
GGB36331_SGB15121 -0.2099425 0.0563573 -0.4256832 0.0057981
Hungatella_hathewayi -0.3753375 0.0883542 -0.8080524 0.0573775
TM7_phylum_sp_oral_taxon_352 0.2849872 0.3473720 -0.3139150 0.8838894
Veillonella_parvula 0.6430477 0.0321454 0.0559377 1.2301577
GGB6649_SGB9391 0.0682979 0.7049816 -0.2886098 0.4252055
Veillonella_atypica -0.0713555 0.8322438 -0.7379991 0.5952881
Open code

if (file.exists("gitignore/result_microbiom_validation.csv") == FALSE) {
  write.table(result_microbiome_val,
    "gitignore/result_microbiom_validation.csv",
    row.names = FALSE
  )
}

6.2.2 Forest plot

6.2.2.1 Prepare data

Open code
## relevant microbiome
diet_sensitive_microbiome <- result_microbiome %>%
  filter(
    fdr_VGdiet_avg < 0.1,
    outcome %in% common_microbiome
  ) %>%
  select(
    outcome
  )

len <- nrow(diet_sensitive_microbiome)

## subset result tables
result_microbiome_subset <- result_microbiome %>%
  filter(outcome %in% diet_sensitive_microbiome$outcome,
         outcome %in% common_microbiome)

result_microbiome_val_subset <- result_microbiome_val %>%
  filter(outcome %in% diet_sensitive_microbiome$outcome,
         outcome %in% common_microbiome)

## create a data frame
data_forest <- data.frame(
  outcome = rep(diet_sensitive_microbiome$outcome, 3),
  beta = c(
    result_microbiome_subset$logFD_VGdiet_inCZ,
    result_microbiome_subset$logFD_VGdiet_inIT,
    result_microbiome_val_subset$logFD_VGdiet
  ),
  lower = c(
    result_microbiome_subset$CI_L_VGdiet_inCZ,
    result_microbiome_subset$CI_L_VGdiet_inIT,
    result_microbiome_val_subset$CI_L_VGdiet
  ),
  upper = c(
    result_microbiome_subset$CI_U_VGdiet_inCZ,
    result_microbiome_subset$CI_U_VGdiet_inIT,
    result_microbiome_val_subset$CI_U_VGdiet
  ),
  dataset = c(
    rep("CZ", len),
    rep("IT", len),
    rep("Validation", len)
  )
)

6.2.2.2 Create forest plot

Open code
colors <- c("CZ" = "#150999", "IT" = "#329243", "Validation" = "grey60")

# Create the forest plot
ggplot(data_forest, aes(x = outcome, y = beta, ymin = lower, ymax = upper, color = dataset)) +
  geom_pointrange(position = position_dodge(width = 0.5), size = 0.5) +
  geom_hline(yintercept = 0, color = 'black') +
  geom_errorbar(position = position_dodge(width = 0.5), width = 0.2) +
  scale_color_manual(values = colors) +
  labs(
    y = "Effect of vegan diet on log2-trasformed microbiome level", 
    x = "Outcome", 
    color = "Dataset"
  ) +
  theme_minimal() +
  coord_flip() +  # Flip coordinates to have outcomes on the y-axis
  theme(
    axis.text.x = element_text(size = 10),
    axis.text.y = element_text(size = 10),
    axis.title.x = element_text(size = 12),
    axis.title.y = element_text(size = 12),
    legend.position = "bottom"
  )  

The forest plot illustrates the effects of a vegan diet on the CLR-transformed read counts of selected bacteria, along with their 95% confidence intervals, across two training cohorts (Czech and Italian) and one independent Czech cohort (external validation). Green points/lines represent differences in CLR-transformed bacterial read counts between vegans and omnivores within the Italian cohort; blue points/lines represent the same difference within the Czech cohort; grey points/lines represent the same difference within the Czech external validation cohort. Positive values suggest a higher count in vegans compared to omnivores. Only bacteria that showed significant differences between vegan and omnivorous diets (as an average effect across both training cohorts) were selected, and these effects were further validated in the independent cohort. The estimates for the training cohorts were obtained from a single linear model that included Diet, Country, and the interaction term Diet:Country as predictors. In the independent Czech validation cohort, Diet was the only fixed-effect predictor

7 Reproducibility

Open code
sessionInfo()
## R version 4.4.2 (2024-10-31)
## Platform: x86_64-pc-linux-gnu
## Running under: Ubuntu 22.04.5 LTS
## 
## Matrix products: default
## BLAS:   /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.10.0 
## LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.10.0
## 
## locale:
##  [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
##  [3] LC_TIME=cs_CZ.UTF-8        LC_COLLATE=en_US.UTF-8    
##  [5] LC_MONETARY=cs_CZ.UTF-8    LC_MESSAGES=en_US.UTF-8   
##  [7] LC_PAPER=cs_CZ.UTF-8       LC_NAME=C                 
##  [9] LC_ADDRESS=C               LC_TELEPHONE=C            
## [11] LC_MEASUREMENT=cs_CZ.UTF-8 LC_IDENTIFICATION=C       
## 
## time zone: Europe/Prague
## tzcode source: system (glibc)
## 
## attached base packages:
## [1] stats     graphics  grDevices utils     datasets  methods   base     
## 
## other attached packages:
##  [1] MicrobiomeStat_1.2 glmnet_4.1-8       pROC_1.18.0        arm_1.12-2        
##  [5] lme4_1.1-35.5      Matrix_1.7-0       MASS_7.3-61        car_3.1-2         
##  [9] carData_3.0-5      emmeans_1.10.4     brms_2.21.0        Rcpp_1.0.13       
## [13] rms_6.8-1          Hmisc_5.1-3        glmmTMB_1.1.9      ggdist_3.3.2      
## [17] cowplot_1.1.1      ggpubr_0.4.0       sjPlot_2.8.16      kableExtra_1.4.0  
## [21] flextable_0.9.6    gtsummary_2.0.2    compositions_2.0-8 janitor_2.2.0     
## [25] stringi_1.7.6      lubridate_1.8.0    forcats_1.0.0      stringr_1.5.1     
## [29] dplyr_1.1.4        purrr_1.0.2        readr_2.1.2        tidyr_1.3.1       
## [33] tibble_3.2.1       ggplot2_3.5.1      tidyverse_1.3.1    readxl_1.3.1      
## [37] openxlsx_4.2.5     RJDBC_0.2-10       rJava_1.0-6        DBI_1.1.2         
## 
## loaded via a namespace (and not attached):
##   [1] fs_1.6.4                matrixStats_1.3.0       httr_1.4.2             
##   [4] insight_0.20.2          numDeriv_2016.8-1.1     tools_4.4.2            
##   [7] backports_1.5.0         sjlabelled_1.2.0        utf8_1.2.4             
##  [10] R6_2.5.1                mgcv_1.9-1              withr_3.0.1            
##  [13] Brobdingnag_1.2-7       prettyunits_1.1.1       gridExtra_2.3          
##  [16] bayesm_3.1-6            quantreg_5.98           cli_3.6.3              
##  [19] textshaping_0.3.6       performance_0.12.2      officer_0.6.6          
##  [22] sandwich_3.0-1          labeling_0.4.2          mvtnorm_1.1-3          
##  [25] robustbase_0.93-9       polspline_1.1.25        ggridges_0.5.3         
##  [28] askpass_1.1             QuickJSR_1.3.1          systemfonts_1.0.4      
##  [31] StanHeaders_2.32.10     foreign_0.8-86          gfonts_0.2.0           
##  [34] svglite_2.1.0           rstudioapi_0.16.0       httpcode_0.3.0         
##  [37] generics_0.1.3          shape_1.4.6             distributional_0.4.0   
##  [40] zip_2.2.0               inline_0.3.19           loo_2.4.1              
##  [43] fansi_1.0.6             abind_1.4-5             lifecycle_1.0.4        
##  [46] multcomp_1.4-18         yaml_2.3.5              snakecase_0.11.1       
##  [49] grid_4.4.2              promises_1.2.0.1        crayon_1.5.0           
##  [52] lattice_0.22-5          haven_2.4.3             pillar_1.9.0           
##  [55] knitr_1.48              statip_0.2.3            boot_1.3-30            
##  [58] estimability_1.5.1      codetools_0.2-19        glue_1.7.0             
##  [61] V8_4.4.2                fontLiberation_0.1.0    data.table_1.15.4      
##  [64] vctrs_0.6.5             cellranger_1.1.0        gtable_0.3.0           
##  [67] assertthat_0.2.1        datawizard_0.12.2       xfun_0.46              
##  [70] mime_0.12               coda_0.19-4             modeest_2.4.0          
##  [73] survival_3.7-0          timeDate_3043.102       iterators_1.0.14       
##  [76] statmod_1.4.36          ellipsis_0.3.2          TH.data_1.1-0          
##  [79] nlme_3.1-165            fontquiver_0.2.1        rstan_2.32.6           
##  [82] fBasics_4041.97         tensorA_0.36.2.1        TMB_1.9.14             
##  [85] rpart_4.1.23            colorspace_2.0-2        nnet_7.3-19            
##  [88] tidyselect_1.2.1        processx_3.8.4          timeSeries_4032.109    
##  [91] compiler_4.4.2          curl_4.3.2              rvest_1.0.2            
##  [94] htmlTable_2.4.0         SparseM_1.81            xml2_1.3.3             
##  [97] fontBitstreamVera_0.1.1 posterior_1.6.0         checkmate_2.3.2        
## [100] scales_1.3.0            DEoptimR_1.0-10         callr_3.7.6            
## [103] spatial_7.3-15          digest_0.6.37           minqa_1.2.4            
## [106] rmarkdown_2.27          htmltools_0.5.8.1       pkgconfig_2.0.3        
## [109] base64enc_0.1-3         stabledist_0.7-2        dbplyr_2.1.1           
## [112] fastmap_1.2.0           rlang_1.1.4             htmlwidgets_1.6.4      
## [115] shiny_1.9.1             farver_2.1.0            zoo_1.8-9              
## [118] jsonlite_1.8.8          magrittr_2.0.3          Formula_1.2-4          
## [121] bayesplot_1.8.1         munsell_0.5.0           gdtools_0.3.7          
## [124] stable_1.1.6            plyr_1.8.6              pkgbuild_1.3.1         
## [127] parallel_4.4.2          ggrepel_0.9.5           sjmisc_2.8.10          
## [130] ggeffects_1.7.0         splines_4.4.2           hms_1.1.1              
## [133] sjstats_0.19.0          ps_1.7.7                uuid_1.0-3             
## [136] ggsignif_0.6.3          stats4_4.4.2            rmutil_1.1.10          
## [139] rstantools_2.1.1        crul_1.5.0              reprex_2.0.1           
## [142] evaluate_1.0.0          RcppParallel_5.1.8      modelr_0.1.8           
## [145] nloptr_2.0.0            tzdb_0.2.0              foreach_1.5.2          
## [148] httpuv_1.6.5            MatrixModels_0.5-3      openssl_1.4.6          
## [151] clue_0.3-65             broom_1.0.6             xtable_1.8-4           
## [154] rstatix_0.7.0           later_1.3.0             viridisLite_0.4.0      
## [157] ragg_1.2.1              lmerTest_3.1-3          cluster_2.1.6          
## [160] bridgesampling_1.1-2

References

Lenth, Russell V. 2024. “Emmeans: Estimated Marginal Means, Aka Least-Squares Means.” https://CRAN.R-project.org/package=emmeans.